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A python extension for quick access to bigWig and bigBed files

License: MIT License

C 93.66% Python 6.34%

bigbed bigwig bioinfomatics

pybigwig's Introduction

deepTools

User-friendly tools for exploring deep-sequencing data

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

For support or questions please post to Biostars. For bug reports and feature requests please open an issue on github.

Citation:

Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 2016 Apr 13:gkw257.

Documentation:

Our documentation contains more details on the individual tool scopes and usages and an introduction to our deepTools Galaxy web server including step-by-step protocols.

Please see also the FAQ, which we update regularly. Our Gallery may give you some more ideas about the scope of deepTools.

For more specific troubleshooting, feedback, and tool suggestions, please post to Biostars.

Installation

deepTools are available for:

Command line usage (via pip / conda / github)
Integration into Galaxy servers (via toolshed/API/web-browser)

There are many easy ways to install deepTools. More details can be found here.

In Brief:

Install through pypi

$ pip install deeptools

Install via conda

$ conda install -c bioconda deeptools

Install by cloning the repository

$ git clone https://github.com/deeptools/deepTools
$ cd deepTools
$ pip install .

Galaxy Installation

deepTools can be easily integrated into Galaxy. Please see the installation instructions in our documentation for further details.

Note: From version 2.3 onwards, deepTools support python3.

This tool suite is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.

Documentation | deepTools Galaxy | FAQ

pybigwig's People

Contributors

Stargazers

Watchers

pybigwig's Issues

AttributeError: 'NoneType' object has no attribute 'split'

hello,

i'm new to python and trying to install this package. I already tried to install it through pip and through the pycharm gui.
i get this error:

Collecting pyBigWig
Using cached pyBigWig-0.3.4.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\sarin\AppData\Local\Temp\pycharm-packaging\pyBigWig\setup.py", line 21, in
for e in sysconfig.get_config_vars('BLDLIBRARY')[0].split():
AttributeError: 'NoneType' object has no attribute 'split'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\sarin\AppData\Local\Temp\pycharm-packaging\pyBigWig\

is there something im missing? and how could i fix this issue?

thanks allot in advance

Segfaults under OSX with conda and python 3

For some unknown reason, OSX builds using python3 and conda are suddenly causing a segfault. This is breaking deepTools as well.

Segmentation fault when opening certain bigwig files

Hey,

I have a couple of BigWig files that mysteriously lead to instant segfaults when I open them using pyBigWig. The one thing these files have in common, is that they are ChIP tracks aligned to the Drosophila r6.07 genome. Maybe there's a problem with some specific chromosome/scaffold names?

import pyBigWig
b = pyBigWig.open("problematic.bw")

Segmentation fault (core dumped)

They convert to bedgraph and back into bigwig using the UCSC tools just fine and I didn't notice any problems with them while browsing in IGV. I uploaded an example file at https://owncloud.gwdg.de/index.php/s/8u0dPjvSqqpQGkv

Thanks for your help!

Problem installing pyBigWig

I tried to install pyBigWig in my mac and I have this error:

pip install git+git://github.com/dpryan79/pyBigWig.git

Collecting git+git://github.com/dpryan79/pyBigWig.git
  Cloning git://github.com/dpryan79/pyBigWig.git to /var/folders/k5/9g2v_yvj2x71jq378t09srm40000gn/T/pip-b6deCA-build
Installing collected packages: pyBigWig
  Running setup.py install for pyBigWig
    Complete output from command /usr/local/opt/python/bin/python2.7 -c "import setuptools, tokenize;__file__='/var/folders/k5/9g2v_yvj2x71jq378t09srm40000gn/T/pip-b6deCA-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/k5/9g2v_yvj2x71jq378t09srm40000gn/T/pip-eJudKT-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_ext
    building 'pyBigWig' extension
    creating build
    creating build/temp.macosx-10.9-x86_64-2.7
    creating build/temp.macosx-10.9-x86_64-2.7/libBigWig
    clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IlibBigWig -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c libBigWig/bwRead.c -o build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwRead.o
    libBigWig/bwRead.c:257:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
            if(rv < 0) goto error;
               ~~ ^ ~
    1 warning generated.
    clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IlibBigWig -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c libBigWig/bwStats.c -o build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwStats.o
    clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IlibBigWig -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c libBigWig/bwValues.c -o build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwValues.o
    clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IlibBigWig -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c libBigWig/io.c -o build/temp.macosx-10.9-x86_64-2.7/libBigWig/io.o
    libBigWig/io.c:109:48: warning: format specifies type 'unsigned long long' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                sprintf(range,"%"PRIu64"-%"PRIu64, pos, pos+URL->bufSize-1);
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
    /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
      __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                           ^
    libBigWig/io.c:109:53: warning: format specifies type 'unsigned long long' but the argument has type 'unsigned long' [-Wformat]
                sprintf(range,"%"PRIu64"-%"PRIu64, pos, pos+URL->bufSize-1);
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
      __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                           ^
    libBigWig/io.c:176:37: warning: format specifies type 'unsigned long long' but the argument has type 'unsigned long' [-Wformat]
            sprintf(range, "0-%"PRIu64, URL->bufSize-1);
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
    /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
      __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                           ^
    3 warnings generated.
    clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -IlibBigWig -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pyBigWig.c -o build/temp.macosx-10.9-x86_64-2.7/pyBigWig.o
    creating build/lib.macosx-10.9-x86_64-2.7
    clang -bundle -undefined dynamic_lookup build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwRead.o build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwStats.o build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwValues.o build/temp.macosx-10.9-x86_64-2.7/libBigWig/io.o build/temp.macosx-10.9-x86_64-2.7/pyBigWig.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -lm -lz -lcurl -lpython2.7 -o build/lib.macosx-10.9-x86_64-2.7/pyBigWig.so
    duplicate symbol _GLOBAL_DEFAULTBUFFERSIZE in:
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwRead.o
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwStats.o
    duplicate symbol _GLOBAL_DEFAULTBUFFERSIZE in:
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwRead.o
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/io.o
    duplicate symbol _GLOBAL_DEFAULTBUFFERSIZE in:
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwRead.o
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwValues.o
    duplicate symbol _GLOBAL_DEFAULTBUFFERSIZE in:
        build/temp.macosx-10.9-x86_64-2.7/libBigWig/bwRead.o
        build/temp.macosx-10.9-x86_64-2.7/pyBigWig.o
    ld: 4 duplicate symbols for architecture x86_64
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    error: command 'clang' failed with exit status 1

    ----------------------------------------
Command "/usr/local/opt/python/bin/python2.7 -c "import setuptools, tokenize;__file__='/var/folders/k5/9g2v_yvj2x71jq378t09srm40000gn/T/pip-b6deCA-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/k5/9g2v_yvj2x71jq378t09srm40000gn/T/pip-eJudKT-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /var/folders/k5/9g2v_yvj2x71jq378t09srm40000gn/T/pip-b6deCA-build

Do you have any idea what could be generating the error? Thanks!

PS. I'm using python 2.7.10 and pip 7.1.2

RuntimeError: Invalid interval bounds!

Running dnasevals=np.array(self.bw.values(chrm,start,end))
with this
chrm=chr2
start=242396100,end=242397100

on this file: https://www.encodeproject.org/files/ENCFF743ULW/@@download/ENCFF743ULW.bigWig (download)

Getting error "RuntimeError: Invalid interval bounds!"

According to hg19 genome length of chr2 is 243199373.

Is this an issue with the Dnase-seq file? How can I check size of chrom with pyBigWig? Thanks so much!

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-eh2hv2_s/pyBigWig/

Hi,

I keep getting this error when i try to install pybigwig on my ubuntu machine with the following command 'pip install pyBigWig==0.3.2'.
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-eh2hv2_s/pyBigWig/

and this error with command 'pip install pyBigWig',

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-pp2reo0g/pybigwig/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-bxqpelh1-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-pp2reo0g/pybigwig/

Any idea why this is happening?

Thanks,
Sandun

[bwGetOverlappingIntervalsCore] Got an error

Thanks for the help on the last error!

The error I get now is:
[bwGetOverlappingIntervalsCore] Got an error
An error occurred while fetching values!

I'm fetching dnase values quickly with a PyTorch dataloader (i.e. bw.values(chrm,start,end)). The error doesn't occur when I'm using the main process (num_workers=0) to fetch the values.

When I set num_workers to 8 like below then I get the error.
loader=DataLoader(valdata,batch_size=20,num_workers=8)

num_workers refers to the number of subprocesses fetching the data.
"how many subprocesses to use for data loading. 0 means that the data will be loaded in the main process (default: 0)" from PyTorch doc.

So I think the error might have to do with simultaneously fetching multiple interval values from the same open file.

Is there anyway to circumvent this? Thanks so much!

Remote content

The underlying C functions support accessing remote files (e.g., via http). Enabling this from within python is quite trivial, but the C code seems to break and then kill python. For example, the following works (after tweaking the C code a bit):

bw = pyBigWig.open("https://rawgit.com/dpryan79/pyBigWig/master/test/test.bw")

But if either the URL doesn't exist or the size of the file isn't returned then Kent's libraries will simply kill everything rather than propagating an error (and returning NULL).

The ideal solution would be to just modify kentlib to behave in a friendlier way, but it's unclear if the license allows distributing modified code (and the bigWig format is weird enough that I really don't want to write a new library to support it).

"Operation now in progress" error when loading remote bigWig files

I was trying to run the example in the README and got the following error:

>>> import pyBigWig
>>> bw = pyBigWig.open("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeCrgMapabilityAlign75mer.bigWig")
>>> bw.stats('chr1', 89294, 91629)
got an error in bwStatsFromZoom in the range 89294-91629: Operation now in progress
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
RuntimeError: An error was encountered while fetching statistics.

I'm using python 2.7 on an Apple:

>>> sys.version
'2.7.11 (default, Nov 17 2016, 17:37:33) \n[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)]'

pip install pyBigWig does not work on latest version of Anaconda (5.3, Python 3.7 version)

I am running on Mac OS X Mojave. Here's the error I get:

Collecting pyBigWig
Using cached https://files.pythonhosted.org/packages/d5/0d/8e2a1edb9524790c6a4d0b70bc800a8e4afee1bc7bdd048c54b8d9cf1c32/pyBigWig-0.3.12.tar.gz
Building wheels for collected packages: pyBigWig
Running setup.py bdist_wheel for pyBigWig ... error
Complete output from command /Users/daquang/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-wheel-hr537bj0 --python-tag cp37:
/Users/daquang/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/init.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing requirements to pyBigWig.egg-info/requires.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
copying pyBigWigTest/test.bigBed -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.bw -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running build_ext
building 'pyBigWig' extension
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64

creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/libBigWig
compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c'
gcc: libBigWig/bwRead.c
gcc: libBigWig/bwValues.cgcc: libBigWig/io.cgcc: libBigWig/bwStats.c
gcc: libBigWig/bwWrite.c
gcc: pyBigWig.c

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrunxcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64 -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c libBigWig/io.c -o build/temp.macosx-10.7-x86_64-3.7/libBigWig/io.o" failed with exit status 1

Failed building wheel for pyBigWig
Running setup.py clean for pyBigWig
Failed to build pyBigWig
Installing collected packages: pyBigWig
Running setup.py install for pyBigWig ... error
Complete output from command /Users/daquang/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-record-w1z6lbxd/install-record.txt --single-version-externally-managed --compile:
/Users/daquang/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/init.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing requirements to pyBigWig.egg-info/requires.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
copying pyBigWigTest/test.bigBed -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.bw -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running build_ext
building 'pyBigWig' extension
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64

creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/libBigWig
compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c'
gcc: libBigWig/bwRead.c
gcc: libBigWig/bwStats.cgcc: libBigWig/io.c
gcc: libBigWig/bwValues.c
gcc: libBigWig/bwWrite.c

gcc: pyBigWig.c
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrunxcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64 -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c libBigWig/bwWrite.c -o build/temp.macosx-10.7-x86_64-3.7/libBigWig/bwWrite.o" failed with exit status 1

----------------------------------------

Command "/Users/daquang/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-record-w1z6lbxd/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/

Hi, I tried all the way to install pybigwig, but all failed

(base) C:\Users\ziywang>conda install -c conda-forge -c bioconda pybigwig
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

pybigwig

Current channels:

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(base) C:\Users\ziywang>conda install pybigwig -c bioconda
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

pybigwig

Current channels:

Return location information when retrieve max value?

Hi,

Sorry, I think it is a simple question but I could not find it in documentation. Is it possible that I could retrieve the corresponding position when try to identify the max value of a region?

bw.stats("chr1",72392,75996,type="max")

Thanks for your help!

Peer certificate cannot be authenticated with given CA certificates

I get the following error when trying to open a remote file:

>>> bw = pyBigWig.open("https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg19/latest/PhyloCSF+0.bw")
[urlOpen] curl_easy_perform received an error: Peer certificate cannot be authenticated with given CA certificates

I've tried to install new CA certificates on my Mac (El Capitan 10.11.6) by following instructions I found online, but they don't seem to fix the issue so far. Would be grateful for suggestions.

Create wheels?

From the pybigwig main folder (where setup.py is), I have successfully created wheels for pybigwig with:

docker pull quay.io/pypa/manylinux1_x86_64
# or docker pull quay.io/pypa/manylinux1_i686
docker run -it -v (pwd):/io quay.io/pypa/manylinux1_x86_64

and then inside docker:

yum install zlib-devel
yum install curl-devel

for PYBIN in /opt/python/*3[5-7]*/bin; do
    "${PYBIN}/pip" install cython  # install these requirements first
    # "${PYBIN}/pip" install -r /io/requirements.txt
    "${PYBIN}/pip" wheel /io/ -w wheelhouse/
done

for whl in wheelhouse/*.whl; do
    auditwheel repair "$whl" -w /io/wheelhouse/
done

Wheels are in the wheelhouse directory. Would you consider creating wheels and uploading to PyPI?

Perhaps add something about not supporting numpy int/float to the docs?

I converted a pandas df to lists of numpy.int64 (starts, ends) and numpy.float64 (values) with list(df.Starts) etc. This gave strange segfaults. Perhaps you should warn about this in the docs that you need to convert these to proper Python values first with int(numpy_int) and float(numpy_float)? I had no idea what I was doing wrong...

Thanks for the library by the way.

Ps. should it work in parallel? Some c-libs like bx-python do not.

pyBigWig using 30+ cores

Is there any way to limit the number of cores used? I am using pyBigWig within a very simple python script that should not need 30+ cores. Or perhaps there is a UNIX trick I can use when launching my script to use less cores? The script is single-threaded, but I believe pyBigWig is using the extra cores.

RuntimeError: You must supply at least a chromosome!

bigwig.stats(chr, start, end) gives a RuntimeError if start and end are of type numpy.int. This is confusing, since the error message is misleading.

Would you please fix this issue to allow numpy integers to be passed in? This is quite common, especially for those of us using pandas 🐼 :)

Copy over modifications to libBigWig

Before the next release, the modifications here need to be brought into sync with libBigWig.

type="sum" for bw.stats()

Hi,
An additional type='sum' for bw.stats() would be very useful

ImportError: ndefined symbol: PyInt_Check

Hi,

I have got this error:

File "./transcriptome.py", line 6, in <module>
    import pyBigWig
ImportError: /usr/local/lib/python3.4/dist-packages/pyBigWig.cpython-34m.so: undefined symbol: PyInt_Check

Problem with python 3.4 ?

creating a bw file

hello,

I'm writing a script that goes from a bam input to a bw output (it's in my github page if you feel like checking it out, input would be very welcome!).

Right now, my script outputs wiggle "strings" in a subprocess pipe to wigToBigWig(the ucsc utility). This is very convenient since wigtobigwig seems to accept the input with no concerns that the chromosomes are out of order, as long as the input per chromosome is in order

for example:

chromosome 2 start:100 step 1:
1
2
1
chromosome 1 start:100 step 1:
1
2
1
chromosome 2 start:200 step 1:
1
2
1
chromosome 1 start:200 step 1:
1
2
1

works fine because the input for each chromosome is in proper order.

does that work with pyBigWig?

If it does i think it should provide a nice speed boost for my script !

y chromosome in Female error

Throw an error on long chromosomes

Xref: deeptools/deepTools#761

I should also propose a new bigWig version to handle longer chromosomes. It'd "just" be a matter of changing the sizes of all the ints.

Command 'clang' failed with exit status 1

I am attempting to use your 1.6 release version of deepTools, but I run into a problem when attempting to install pyBigWig through pip or by cloning the git repository locally.

I am getting the following error: error: command 'clang' failed with exit status 1
And during the pip install I recieve a similar error with a "Cannot build wheel for pyBigWig" error.

I've searched but can't seem to find a way to fix this. I am using an iMAC OSX El Capitan version 10.11.2. I have the most recent pip installation and setuptools is installed as well as the latest Xcode and command line tools. My clang version is Apple LLVM version 7.0.2 (clang-700.1.81) Target: x86_64-apple-darwin15.2.0 Thread model: posix

Thanks,

Incorrect check of malloc result

pyBigWig/libBigWig/bwRead.c

Line 76 in 0f1b4fd

if(!dataOffset) {

Allocation is done for indexOffset and the check is for dataOffset variable. Probable result of copy/paste.

Error: Mismatch in the magic number

I wanted to explore the API, creating a bigWig file, adding a header and entries, and getting some values back from it:

#!/usr/bin/env python

import pyBigWig

bw = pyBigWig.open("/tmp/foo.bw", "w")
bw.addHeader([("chr1", 1000000)], maxZooms=0)
bw.addEntries(["chr1", "chr1", "chr1"], [0, 100, 125], ends=[5, 120, 126], values=[0.0, 1.0, 200.0])
bw.values("chr1", 0, 126)

When I run the above, I get the following error:

[readRTreeIdx] Mismatch in the magic number!
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
RuntimeError: An error occurred while fetching values!

Am I missing a step in how to add and retrieve values?

Segmentation fault: 11 on MacOS High Sierra 10.13.3

I did a completely fresh install of Anaconda3 and then installed pyBigWig using

conda install -c bioconda deeptools

When I ran import pyBigWig I got a Segmentation fault: 11 error.

This issue does not exist on my Ubuntu 16.04 computer.

No 0.2.3 release is tagged

Unable to open bigBed files

I have been unable to open bigBed files, both local and remote. Opening bigWig files works just fine. Using the example bigBed opening in the documentation, I get the following error:

$ python -c "import pyBigWig; pyBigWig.open('ENCFF001JBR.bigBed')"

[bwHdrRead] There was an error while reading in the header!
Traceback (most recent call last):
  File "<string>", line 1, in <module>
RuntimeError: Received an error during file opening!

The bigBed was downloaded successfully and appears normal based on the bigBedInfo results:

$ bigBedInfo ENCFF001JBR.bigBed

version: 4
fieldCount: 9
hasHeaderExtension: yes
isCompressed: yes
isSwapped: 0
extraIndexCount: 0
itemCount: 602,461
primaryDataSize: 10,164,686
primaryIndexSize: 46,456
zoomLevels: 10
chromCount: 21
basesCovered: 422,391,811
meanDepth (of bases covered): 1.040633
minDepth: 1.000000
maxDepth: 2.000000
std of depth: 0.197439

Is there an additional bigBed library I need to have installed? Does opening bigBed files require a substantially greater amount of memory? (currently have ~40 GB available)

wrong 'stats' output?

Thanks for developing pyBigWig, this is a very useful module. I've noticed some instances where 'stats' returns an incorrect value (compared with taking the mean of the values returned by 'values'). Here's an example, using an ENCODE mappability track:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeCrgMapabilityAlign75mer.bigWig

bw = pyBigWig('wgEncodeMapability/wgEncodeCrgMapabilityAlign75mer.bigWig')
mean(bw.values('chr1', 89294, 91629))
>> 0.22213842662134081
bw.stats('chr1', 89294, 91629)
>> [0.1902993809998163]

Thanks in advance for looking into this.

addEntries

I get the following error:

RuntimeError: The entries you tried to add are out of order, precede already added entries, or otherwise use illegal values.

The problem is that I sort my lists and then add the entries.

Does not compile without curl

Building release 0.3.13 using python 3 fails due to a bug in setup.py:

Traceback (most recent call last):
  File "nix_run_setup", line 8, in <module>
    exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))
  File "setup.py", line 43, in <module>
    foo = foo.decode().strip().split()
AttributeError: 'str' object has no attribute 'decode'

Under python 3 there is no need to decode UTF-8 strings. Modifying the offending line to foo = foo.strip().split() resolves the problem.

can't create a bigwig file

When I try to create a bigwig file from numpy data, I get an error. Here is the code

import pyBigWig
import numpy as np
bw = pyBigWig.open("delete.bw", "w")
bw.addHeader([("chr1", 100), ("chr2", 100)])
chroms = np.array(["chr1"] * 4 + ["chr2"] * 4)
starts = np.array([0, 10, 40, 50, 60, 70, 80, 90], dtype=np.int64)
ends = np.array([5, 15, 45, 55, 65, 75, 85, 95], dtype=np.int64)
values0 = np.array(np.random.random_sample(8), dtype=np.float64)
bw.addEntries(chroms, starts, ends=ends, values=values0)
bw.close()

and here is the error

Traceback (most recent call last):
  File "/home/rick/anaconda3/envs/tensorflow/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2910, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-2-e11cdb4af2f6>", line 9, in <module>
    bw.addEntries(chroms, starts, ends=ends, values=values0)
RuntimeError: The entries you tried to add are out of order, precede already added entries, or otherwise use illegal values.
 Please correct this and try again

I checked whether pyBigWig was installed with numpy

pyBigWig.numpy
Out[6]: 1

Now if I add validate false flag,
bw.addEntries(chroms, starts, ends=ends, values=values0, validate=False)

I get this warning but the file saves correctly

[bwClose] There was an error while finishing writing a bigWig file! The output is likely truncated.

The version I am using is pybigwig 0.3.9 np113py36_0 bioconda

Installing on different directory

I'm trying to install pyBigWig with pip (python 3.5) on a different directory then the default one (I have no root access, and home directory has limited space)

It seems that the setup.py doesn't support neither --target nor --prefix. ( http://stackoverflow.com/questions/2915471/install-a-python-package-into-a-different-directory-using-pip )

 pip install --target=~/pysitePackages/ pyBigWig
 /usr/lib/python3/dist-packages/pip/commands/install.py:198: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
   cmdoptions.check_install_build_global(options)
 Collecting pyBigWig
   Using cached pyBigWig-0.2.8.tar.gz
 Skipping bdist_wheel for pyBigWig, due to binaries being disabled for it.
 Installing collected packages: pyBigWig
   Running setup.py install for pyBigWig ... error
     Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-g8_x12wg/pyBigWig/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-vz5xa_zy-record/install-record.txt --single-version-externally-managed --compile "\"--target=~/pysitePackages/\"" --user --prefix= --home=/tmp/tmpu3rg1ts8:
     /usr/lib/python3.5/distutils/dist.py:261: UserWarning: Unknown distribution option: 'classifier'
       warnings.warn(msg)
     invalid command name '"--target=~/pysitePackages/"'

For now I work around it by installing it directly from source.

Thanks

Accessing ENCODE files on Mac; issue with curl?

In the README, an ENCODE bigBed file is opened. On Linux, I'm able to run the command as written:

>>> import pyBigWig
>>> bb = pyBigWig.open("https://www.encodeproject.org/files/ENCFF001JBR/@@download/ENCFF001JBR.bigBed")

On Mac, I'm receiving the following error:

>>> import pyBigWig
>>> bb = pyBigWig.open("https://www.encodeproject.org/files/ENCFF001JBR/@@download/ENCFF001JBR.bigBed")
[urlOpen] curl_easy_perform received an error: Peer certificate cannot be authenticated with given CA certificates
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
RuntimeError: Received an error during file opening!

I'm still able to access the file using my browser.

Trying to fix the issue, I updated my installation of curl (now 7.52.1) but am still getting the error. I ran curl with the file, and it seems like there is a redirect:

$ curl https://www.encodeproject.org/files/ENCFF001JBR/@@download/ENCFF001JBR.bigBed
<html>
 <head>
  <title>307 Temporary Redirect</title>
 </head>
 <body>
  <h1>307 Temporary Redirect</h1>
  The resource has been moved to https://download.encodeproject.org/http://encode-files.s3.amazonaws.com/2012/07/30/40ee5859-5afc-46b8-a4e5-9779669a5051/ENCFF001JBR.bedRnaElements.bigBed?Signature=HiyYAGlS1jZP2ffhK46Op%2B1hQXQ%3D&amp;Expires=1485926876&amp;AWSAccessKeyId=ASIAITRX7ADMF5IN73PA&amp;response-content-disposition=attachment%3B%20filename%3DENCFF001JBR.bigBed&amp;x-amz-security-token=FQoDYXdzEHkaDLO1lA56pGNBt180RyKcAymTGbyRfgD6/Dd/ACwRyDEoeSRkqrEwuOaOvo3SUg9re/zmv7XpMQowGhuHqtlbz1oLjj%2BBX4CZesx4DJzhs8nJep1APd9vvYmV5PekS2MKZM4/7GWlbOqAKYfJUtSQWq/NGjHtwaFJz1fhG2HKJQMyGuZxyW5goH%2Bi8MOLqYo8Md49BLJGhCJ89F12HRTUzsVDKyo1bbrx5YsT2/9hAmyP1qihgj2uFP9dBs/LUudwtx%2BWvdleLlJ1fbVLy3rWMzd1rjv%2B1%2B6/Vg146ukHraoKekz4c9lnztGoZPukA9Tjd3sXfz1Lb1/H8ZqHbZO/yjAR3RwILpdT%2BVG8DUNo9GuPxLhai1v9s6S1%2BYt3HnvRtL/rNYWtdGVIAdDW6QhjvgmaqO6qNAf0PkoE33EWl34TENBXxOfrZ8VOwEUDUxPLI5G6iebW8Kwknj1F/XR6hUJpoGmDGrDpAU54FG/pf4NmlMAqa2fE9/xcJYxAZPs36Arm2v%2BThSfYvLlHz/yvEWwq3G6YaxUk5P8vMjBRGTd41RgypvBA%2BSGk5scoyM%2B9xAU%3D; you should be redirected automatically.


 </body>
</html>

Could this be contributing to my issue?

Allow pyBigWig.open() in with statement.

It would be nice if pyBigWig.open() could be used with the with statement:

with pyBigWig.open('ENCFF001LFU.broadPeak.bigbed', 'rb') as bb:
    print(bb.header())

It is missing __exit__ and __enter__ methods.

pyBigWig does not install through install_requires for python package

Hi,

I want to set pyBigWig as an installation dependency for my own python package using install_requires in setup.py, but I am having trouble during the installation procedure.

My minimal setup.py looks like this:

from setuptools import setup
setup(name='mypackage',
      install_requires=["pyBigWig"])

Upon python setup.py install I get the following messages/errors:

Processing dependencies for mypackage==0.0.0
Searching for pyBigWig
Reading https://pypi.org/simple/pyBigWig/
Downloading https://files.pythonhosted.org/packages/5c/9c/2e01d04b6fd31c1e09537c8f51410123c087da4974bdb0fcdb7ec25dab62/pyBigWig-0.3.13.tar.gz#sha256=c65cb9ccd78a4ede00c3209579173e4f7e67598daf6dc079676a0e8982163f5b
Best match: pyBigWig 0.3.13
Processing pyBigWig-0.3.13.tar.gz
Writing /tmp/easy_install-swqddsi0/pyBigWig-0.3.13/setup.cfg
Running pyBigWig-0.3.13/setup.py -q bdist_egg --dist-dir /tmp/easy_install-swqddsi0/pyBigWig-0.3.13/egg-dist-tmp-r3gwo7hc
/home/mbentse/.conda/envs/mypackage_env/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
  warnings.warn(msg)
zip_safe flag not set; analyzing archive contents...
__pycache__.pyBigWig.cpython-37: module references __file__
pyBigWigTest.__pycache__.test.cpython-37: module references __file__
No eggs found in /tmp/easy_install-swqddsi0/pyBigWig-0.3.13/egg-dist-tmp-r3gwo7hc (setup script problem?)
error: The 'pyBigWig' distribution was not found and is required by mypackage

Strangely pip install pybigwig works, but I would love for it to recognize the package automatically so that I don't have to handle the exception when importing pybigwig later on.

Hope you can help out with a solution!

Write out bw track color?

Not so much an issue but was curious if it was possible to write out a bw track with a specific color for visualization on IGV? Perhaps this can be integrated into the header?

Test OSX fix with continuum conda and release a bugfix version

This serves as a reminder to me, mostly. I need to test the most recent PR and release a bugfix version. I should then implement that in py2bit and deeptoolsintervals, releasing bugfix versions of those too (granted, no one has run into this there, but for the sake of consistency...).

Issue loading pyBigWig within conda environment

Hi,

I've seen a few issues resolved that related to libcurl. However, I can't find a solution to my current issue. Does that look any familiar?

$ python
Python 3.6.2 | packaged by conda-forge | (default, Jul 23 2017, 22:59:30) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyBigWig
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: /gfs/devel/kralbrecht/miniconda3/envs/py362/lib/libcurl.so.4: undefined symbol: libssh2_scp_recv2

I've tried installing pyBigWig using both pip and conda install. Both of them report a successful installation, yet result in the same error.
In both cases I seem to have the latest version installed:

pybigwig                  0.3.5               np112py36_0    bioconda

Let me know if you need additional details about the system (e.g., other package versions installed in the environment). I've updated them all the latest, using conda update --all, but that didn't solve the issue.

Many thanks in advance,
Kevin

undefined symbol: hasEntries

Using version 0.3.5 I'm getting this error when importing pyBigWig (Python 2.7.9 on Ubuntu 15.04):

ImportError: /home/chug/kaic_venv/local/lib/python2.7/site-packages/pyBigWig.so: undefined symbol: hasEntries

I installed it using the binary wheel from PyPI. The symbol hasEntries doesn't seem to be properly exported:

> readelf -a /home/chug/kaic_venv/local/lib/python2.7/site-packages/pyBigWig.so | grep hasEntries
000000216038  000600000007 R_X86_64_JUMP_SLO 0000000000000000 hasEntries + 0
      6: 0000000000000000     0 NOTYPE  GLOBAL DEFAULT  UND hasEntries
    100: 0000000000000000     0 NOTYPE  GLOBAL DEFAULT  UND hasEntries

Interestingly, when I install from source using pip install --no-binary :all: pyBigWig it works fine.

libcurl3/4 issue on Ubuntu machine

This is an ongoing problem with many packages with a transition from libcurl3 to libcurl4 in Ubuntu: deeptools does not run due to:
ImportError: /usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /usr/local/lib/python2.7/dist-packages/pyBigWig.so)

is there a way to fix this other than reverting to libcurl3 (and breaking a host of mostly R packages in the process)?

Allow files with no entries

pyBigWig throws an error if you try to create a bigWig with only a header. bedGraphToBigWig produces a mostly empty file that it can't open either. Ideally there should just be a variant that could be meaningfully understood to be "just a header".

Install without libcurl

We are not using the libcurl features, but it is stopping our installations looking for curl-config. We would like to be able to use PyBigWig without the system providing this binary. It is currently breaking our docs build on RTD. https://readthedocs.org/projects/ga4gh-reference-implementation/builds/5120992/

Is it possible to package it without those requirements?

isBigWig segfault

pyBigWig.isBigWig(1) and pyBigWig.isBigBed(1) cause segfaults using Python 2, Python 3 seems unaffected. Tested on Mac and Ubuntu.

Also, maybe related, it seems that in Python 2 pyBigWig.pyBigWig is not exported.

Issues with 10s of thousands of contigs

From the deepTools mailing list, it seems that bigWig files with 10s of thousands of contigs can't be created in any sensible way. I actually wonder if this is related to how the internal index works, since each contig needs to be its own leaf on a node. If the top-level node can't hold that many leaves then perhaps that's the problem (I though I'd fixed that issue though).

pyBigWig can't open Path objects

This should probably work in python3 but doesn't

from pathlib import Path
import pyBigWig

bw = Path("test.bw")
pyBigWig.open(bw )

Problem with pyBigWig installation

Hello,
I tried to install pyBigWig on linux using the following command:

pip install pyBigWig --user

Unfortunately I get this error:

Collecting pyBigWig
Using cached pyBigWig-0.3.2.tar.gz
Complete output from command python setup.py egg_info:
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py:257: UserWarning: Unbuilt egg for pyBigWig [unknown version] (/tmp/pip-build-QTHkvJ/pyBigWig)
ep.require(installer=self.fetch_build_egg)
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-build-QTHkvJ/pyBigWig/setup.py", line 84, in
ext_modules = [module1])
File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
_setup_distribution = dist = klass(attrs)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 272, in fetch_build_egg
dist = self.class({'script_args':['easy_install']})
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 225, in init
_Distribution.init(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in init
self.finalize_options()
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2029, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 579, in resolve
env = Environment(self.entries)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 748, in init
self.scan(search_path)
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 777, in scan
for dist in find_distributions(item):
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 1757, in find_on_path
path_item,entry,metadata,precedence=DEVELOP_DIST
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2151, in from_location
py_version=py_version, platform=platform, **kw
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 2128, in init
self.project_name = safe_name(project_name or 'Unknown')
File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 1139, in safe_name
return re.sub('[^A-Za-z0-9.]+', '-', name)
RuntimeError: maximum recursion depth exceeded

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-QTHkvJ/pyBigWig/

I use this python version:
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.

Any help is very much appreciated. This is actually my first "help" post. If you need more information or have suggestions how I can improve my question I am very open for suggestions.

Best wishes,
Stefano

Parallelizing pyBigWig.values()

Hi there,

First of all, I'd like to say that pyBigWig and Deeptools are awesome tools. Thanks a lot for creating them.

I have been trying to parallelize pyBigWig.values() with the multiprocessing library without success. Essentially what I tried to do is something like this

import pyBigWig
import pandas as pd
from multiprocessing import Pool

bw = pyBigWig.open("/path/to/bigwig.bw")
coordinates = [(0, ["chr1", 120000, 130001]), (1, ["chr3", 160000, 170001]), etc...]
counts = pd.DataFrame(columns=[i for i in range(10001)])

def extract_data(data):
    index, row = data
    counts.loc[index] = pd.Series(bw.values(row[0], row[1], row[2])).fillna(0).astype(int)

pool = Pool(n)
pool.map(extract_data, coordinates)

Which works fine if n = 1, but for n > 1, I receive an error saying that there was a problem getting values.

Any ideas as to how to accomplish this?

Thanks a lot in advance

problem with installing pyBigWig

Hello,
I tried to install pyBigWig on linux in order to use deeptools 2, unfortunately I get these errors:

Linux distribution I am using
Description: Ubuntu 14.04.3 LTS
Release: 14.04
Codename: trusty

python I am using
Python 2.7.6 (default, Jun 22 2015, 17:58:13)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.

I am unsure here what more information I should provide

The errors: #1

simon@simon-Aspire-E1-572:~$ sudo -H pip install git+git://github.com/dpryan79/pyBigWig.git
Collecting git+git://github.com/dpryan79/pyBigWig.git
Cloning git://github.com/dpryan79/pyBigWig.git to /tmp/pip-9zWXyi-build
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-9zWXyi-build/setup.py", line 24, in
foo, _ = subprocess.Popen(['curl-config', '--libs'], stdout=subprocess.PIPE).communicate()
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-9zWXyi-build

Error #2

When I am trying to install it "directly" in the folder where I downloaded it, I get this error:

simon@simon-Aspire-E1-572:~/Downloads/pyBigWig-0.2.3$ python setup.py install
Traceback (most recent call last):
File "setup.py", line 24, in
foo, _ = subprocess.Popen(['curl-config', '--libs'], stdout=subprocess.PIPE).communicate()
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory