installation on MAC about pipeline HOT 9 CLOSED

Hi @nbahlis , sorry for the delayed response.

Did you try following these detailed build instructions, which includes build instructions of Mac OS?

https://github.com/BradnerLab/pipeline/wiki/bamliquidator#check-list

It looks like you either don't have samtools installed or it isn't configured properly so the linker can't find libbam.a.

If this doesn't help, can you please type into your terminal brew info samtools and reply back with the output?

Thanks

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thank you John for your reply. that’s what I get for brew info samtools:

homebrew/science/samtools: stable 1.2 (bottled), HEAD
http://www.htslib.org/
/usr/local/Cellar/samtools/1.2 (44 files, 1.2M) *
Poured from bottle
From: https://github.com/homebrew/homebrew-science/blob/master/samtools.rb
==> Dependencies
Required: htslib ✔
Optional: dwgsim ✘
==> Options
--with-dwgsim
Build with Whole Genome Simulation
--without-curses
Skip use of libcurses, for platforms without it, or different curses naming
--HEAD
Install HEAD version

thank you
nizar

On Nov 30, 2015, at 9:00 PM, John DiMatteo [email protected] wrote:

Hi @nbahlis https://github.com/nbahlis , sorry for the delayed response.

Did you try following these detailed build instructions, which includes build instructions of Mac OS?

https://github.com/BradnerLab/pipeline/wiki/bamliquidator#check-list https://github.com/BradnerLab/pipeline/wiki/bamliquidator#check-list
It looks like you either don't have samtools installed or it isn't configured properly so the linker can't find libbam.a.

If this doesn't help, can you please type into your terminal brew info samtools and reply back with the output?

Thanks

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Reply to this email directly or view it on GitHub #53 (comment).

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Sorry I haven't built on a Mac in a while and I'm afraid that the makefile needs changes to work with the current version of samtools.

Can you please try adding -lhts to the makefile? Change this line of bamliquidator_internal/makefile

LDLIBS := -lbam -lz -lpthread

to this:

LDLIBS := -lbam -lz -lpthread -lhts

Unfortunately I won't have access to a mac for a few days, so I can't test this myself. If you can hold on for a few more days, I will test building on the mac and update the makefile as necessary.

from pipeline.

Thank you John

Adding -lhts seem to have solved the problem. I will do some more testing.

Nizar

On Nov 30, 2015, at 10:25 PM, John DiMatteo [email protected] wrote:

Sorry I haven't built on a Mac in a while and I'm afraid that the makefile needs changes to work with the current version of samtools.

Can you please try adding -lhts to the makefile? Change this line of bamliquidator_internal/makefile

LDLIBS := -lbam -lz -lpthread
to this:

LDLIBS := -lbam -lz -lpthread -lhts
Unfortunately I won't have access to a mac for a few days, so I can't test this myself. If you can hold on for a few more days, I will test building on the mac and update the makefile as necessary.

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Hi Nizar,

You should be all set then. You can run python bamliquidatorbatch/test.py from the bamliquidator_internal directory, and if it ends with "Ran 22 tests in...OK" and exit code 0 then you should feel confident everything is working correctly with your build. (Note that the python tests many error conditions, so please ignore ERROR/WARNING stdout messages -- the exit code of 0 and the "OK" indicates that the tests all passed.)

Regards,
John

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I'll update the make file in a few days so that nobody else runs into the same problem you had.

from pipeline.

thanks John for your help, I had to install tables.

I think the the test.py was fine.Please see below, do I need bokeh

/Users…….../pipeline/bamliquidator_internal/bamliquidatorbatch/normalize_plot_and_summarize.py:243: RuntimeWarning: invalid value encountered in true_divide
percentiles = (stats.rankdata(normalized_count_list) - 1) / (len(normalized_count_list)-1) * 100
ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.ERROR Bin size cannot be zero
.ERROR:root:Skipping plotting because plots require a compatible version of bokeh -- see https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install . Bokeh module not found; consider running the following command to install: sudo pip install bokeh
.WARNING No valid regions detected in /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_jU4hwJ/empty.gff
WARNING No valid regions detected in /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_jU4hwJ/empty.gff
.WARNING Excluding invalid region on line 1: bam file key 1 chr1 region1 60 -> 70 . 0
WARNING No valid regions detected in /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_VTTgij/single.gff
..ERROR Unhandled exception: Not enough columns parsing line 1 '' of /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_CF608r/single.bed
ERROR Unhandled exception: Not enough columns parsing line 1 'chr1' of /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_CF608r/single.bed
ERROR Unhandled exception: Not enough columns parsing line 1 'chr1 1' of /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_CF608r/single.bed
.....WARNING Truncated region on line 1 from 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr' to 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr'
..WARNING Truncated region on line 1 from 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr' to 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr'
..WARNING Excluding invalid region on line 1: bam file key 1 chr10 region1 60 -> 70 . 0
WARNING No valid regions detected in /var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_UpjYae/single.gff

.

Ran 22 tests in 1.811s

OK
Closing remaining open files:/var/folders/wr/q543_lks5wg4bpth7my9nsc00000gn/T/blt_ogBXxZ/output/counts.h5…done

thanks again
nizar

On Dec 1, 2015, at 9:04 AM, John DiMatteo [email protected] wrote:

I'll update the make file in a few days so that nobody else runs into the same problem you had.

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from pipeline.

Hi Nizar,

Your test result indicates that all tests passed.

bokeh is optional, and is used to create html graphs like this: http://jdimatteo.github.io/Meta-Analysis/chr20.html

It is up to you whether or not you want to use the bokeh graphs to visually inspect the output directly, or whether you just need the .txt or .hdf5 bamliquidator output.

Regards,
John

from pipeline.

Super, thanks again John for your help

Nizar

On Dec 1, 2015, at 11:31 PM, John DiMatteo [email protected] wrote:

Hi Nizar,

Your test result indicates that all tests passed.

bokeh is optional, and is used to create html graphs like this: http://jdimatteo.github.io/Meta-Analysis/chr20.html

It is up to you whether or not you want to use the bokeh graphs to visually inspect the output directly, or whether you just need the .txt or .hdf5 bamliquidator output.

Regards,
John

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