Subset of Galaxy (http://galaxyproject.org/) core code designed to be used as a library.
License: Other
A small subset of the Galaxy project for reuse outside the core. This subset has minimal dependencies and is Python 3 compatible.
Seems that galaxy.web.stack is no more?
On macOS High Sierra, executing:
mulled-build build-and-test 'r-seurat-workflow=0.0.1--0' --extra-channel file://Users/pmoreno/miniconda3/conda-bld/ --test 'which read-10x.R' --involucro-path /Users/pmoreno/venvs/mulled/bin/involucro
fails with:
/Users/pmoreno/venvs/mulled/bin/involucro -v=2 -f /Users/pmoreno/venvs/mulled/lib/python2.7/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,file://Users/pmoreno/miniconda3/conda-bld/' -set TEST='which read-10x.R' -set TARGETS='r-seurat-workflow=0.0.1=0' -set REPO='quay.io/biocontainers/r-seurat-workflow:0.0.1--0' -set BINDS='build/dist:/usr/local/,/Users/pmoreno/miniconda3/conda-bld/:/Users/pmoreno/miniconda3/conda-bld/' build-and-test
.No handlers could be found for logger "galaxy.tools.deps.commands"
[Jul 4 11:48:46] DEBU Run file [/Users/pmoreno/venvs/mulled/lib/python2.7/site-packages/galaxy/tools/deps/mulled/invfile.lua]
[Jul 4 11:48:46] INFO Invoke Task [build]
[Jul 4 11:48:46] STEP Run image [continuumio/miniconda3:latest] with command [[rm -rf /data/dist]]
[Jul 4 11:48:46] DEBU Creating container [step-d2ac29a445]
[Jul 4 11:48:46] DEBU Image [continuumio/miniconda3:latest] not present, pulling it
[Jul 4 11:48:46] DEBU Pull Image [continuumio/miniconda3:latest]
[Jul 4 11:49:07] DEBU Created container [9dd653a644bf step-d2ac29a445], starting it
[Jul 4 11:49:07] DEBU Container [9dd653a644bf step-d2ac29a445] started, waiting for completion
[Jul 4 11:49:08] DEBU Container [9dd653a644bf step-d2ac29a445] completed with exit code [0] as expected
[Jul 4 11:49:08] DEBU Container [9dd653a644bf step-d2ac29a445] removed
[Jul 4 11:49:08] STEP Run image [continuumio/miniconda3:latest] with command [[/bin/sh -c conda install -c bioconda -c file://Users/pmoreno/miniconda3/conda-bld/ r-seurat-workflow=0.0.1=0 -p /usr/local --copy --yes --quiet]]
[Jul 4 11:49:08] DEBU Creating container [step-8f97df74f8]
[Jul 4 11:49:08] DEBU Created container [9fa5aa8d945d step-8f97df74f8], starting it
[Jul 4 11:49:09] DEBU Container [9fa5aa8d945d step-8f97df74f8] started, waiting for completion
[Jul 4 11:49:09] SOUT Solving environment: ...working... failed
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR `$ /opt/conda/bin/conda install -c bioconda -c file://Users/pmoreno/miniconda3/conda-bld/ r-seurat-workflow=0.0.1=0 -p /usr/local --copy --yes --quiet`
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR environment variables:
[Jul 4 11:49:10] SERR CIO_TEST=<not set>
[Jul 4 11:49:10] SERR CONDA_ROOT=/opt/conda
[Jul 4 11:49:10] SERR PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin
[Jul 4 11:49:10] SERR :/bin
[Jul 4 11:49:10] SERR REQUESTS_CA_BUNDLE=<not set>
[Jul 4 11:49:10] SERR SSL_CERT_FILE=<not set>
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR active environment : None
[Jul 4 11:49:10] SERR user config file : /root/.condarc
[Jul 4 11:49:10] SERR populated config files :
[Jul 4 11:49:10] SERR conda version : 4.5.4
[Jul 4 11:49:10] SERR conda-build version : not installed
[Jul 4 11:49:10] SERR python version : 3.6.5.final.0
[Jul 4 11:49:10] SERR base environment : /opt/conda (writable)
[Jul 4 11:49:10] SERR channel URLs : https://conda.anaconda.org/bioconda/linux-64
[Jul 4 11:49:10] SERR https://conda.anaconda.org/bioconda/noarch
[Jul 4 11:49:10] SERR file://users/pmoreno/miniconda3/conda-bld/linux-64
[Jul 4 11:49:10] SERR file://users/pmoreno/miniconda3/conda-bld/noarch
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/main/linux-64
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/main/noarch
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/free/linux-64
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/free/noarch
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/r/linux-64
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/r/noarch
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/pro/linux-64
[Jul 4 11:49:10] SERR https://repo.anaconda.com/pkgs/pro/noarch
[Jul 4 11:49:10] SERR package cache : /opt/conda/pkgs
[Jul 4 11:49:10] SERR /root/.conda/pkgs
[Jul 4 11:49:10] SERR envs directories : /opt/conda/envs
[Jul 4 11:49:10] SERR /root/.conda/envs
[Jul 4 11:49:10] SERR platform : linux-64
[Jul 4 11:49:10] SERR user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/4.9.87-linuxkit-aufs debian/9 glibc/2.24
[Jul 4 11:49:10] SERR UID:GID : 0:0
[Jul 4 11:49:10] SERR netrc file : None
[Jul 4 11:49:10] SERR offline mode : False
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR V V V V V V V V V V V V V V V V V V V V V V V V V V V V V V V
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR CondaHTTPError: HTTP 404 CONNECTION FAILED for url <file://users/pmoreno/miniconda3/conda-bld/noarch/repodata.json>
[Jul 4 11:49:10] SERR Elapsed: 00:00.000194
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR The remote server could not find the noarch directory for the
[Jul 4 11:49:10] SERR requested channel with url: file://users/pmoreno/miniconda3/conda-bld
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR As of conda 4.3, a valid channel must contain a `noarch/repodata.json` and
[Jul 4 11:49:10] SERR associated `noarch/repodata.json.bz2` file, even if `noarch/repodata.json` is
[Jul 4 11:49:10] SERR empty. please request that the channel administrator create
[Jul 4 11:49:10] SERR `noarch/repodata.json` and associated `noarch/repodata.json.bz2` files.
[Jul 4 11:49:10] SERR $ mkdir noarch
[Jul 4 11:49:10] SERR $ echo '{}' > noarch/repodata.json
[Jul 4 11:49:10] SERR $ bzip2 -k noarch/repodata.json
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR You will need to adjust your conda configuration to proceed.
[Jul 4 11:49:10] SERR Use `conda config --show channels` to view your configuration's current state.
[Jul 4 11:49:10] SERR Further configuration help can be found at <https://conda.io/docs/config.html>.
[Jul 4 11:49:10] SERR
[Jul 4 11:49:10] SERR A reportable application error has occurred. Conda has prepared the above report.
[Jul 4 11:49:10] SERR Upload successful.
[Jul 4 11:49:11] ERRO Task processing failed: Unexpected exit code [1] of container [9fa5aa8d945d step-8f97df74f8], container preserved
Main error seems to be:
[Jul 4 11:49:10] SERR CondaHTTPError: HTTP 404 CONNECTION FAILED for url <file://users/pmoreno/miniconda3/conda-bld/noarch/repodata.json>
although the file does exist in the host file system:
ls -l ~/miniconda3/conda-bld/noarch/repodata.json
-rw-r--r-- 1 pmoreno staff 61 4 Jul 10:17 /Users/pmoreno/miniconda3/conda-bld/noarch/repodata.json
I presume that there must be an option to add certain directories to the container that I'm missing. I had previously indexed the local channel as suggested here.
Thanks!
planemo mull project_templates/conda_testing/samtools.xml
/Users/john/.planemo/involucro -v=3 -f /Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.5.5.dev0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,conda-forge,r' -set TEST='true' -set TARGETS='samtools=1.3.1' -set REPO='quay.io/biocontainers/samtools:1.3.1' -set BINDS='build/dist:/usr/local/' build
/Users/john/.planemo/involucro -v=3 -f /Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.5.5.dev0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,conda-forge,r' -set TEST='true' -set TARGETS='samtools=1.3.1' -set REPO='quay.io/biocontainers/samtools:1.3.1' -set BINDS='build/dist:/usr/local/' build
[Feb 27 13:44:20] DEBU Run file [/Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.5.5.dev0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua]
[Feb 27 13:44:20] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]]
[Feb 27 13:44:20] DEBU Creating container [step-09b5d695dc]
[Feb 27 13:44:20] DEBU Created container [013d3eda40f3 step-09b5d695dc], starting it
[Feb 27 13:44:20] DEBU Container [013d3eda40f3 step-09b5d695dc] started, waiting for completion
[Feb 27 13:44:21] DEBU Container [013d3eda40f3 step-09b5d695dc] completed with exit code [0] as expected
[Feb 27 13:44:21] DEBU Container [013d3eda40f3 step-09b5d695dc] removed
[Feb 27 13:44:21] STEP Run image [continuumio/miniconda:latest] with command [[/bin/sh -c conda install -c bioconda -c conda-forge -c r samtools=1.3.1 -p /usr/local --copy --yes --quiet]]
[Feb 27 13:44:21] DEBU Creating container [step-2b07baa1fe]
[Feb 27 13:44:21] DEBU Created container [88a2c45c08c6 step-2b07baa1fe], starting it
[Feb 27 13:44:22] DEBU Container [88a2c45c08c6 step-2b07baa1fe] started, waiting for completion
[Feb 27 13:44:28] SOUT Fetching package metadata .............
[Feb 27 13:44:29] SOUT Solving package specifications: ..........
[Feb 27 13:44:55] SERR
[Feb 27 13:44:55] SERR
[Feb 27 13:44:55] SERR CondaOSError: OS error: failed to link (src=u'/opt/conda/pkgs/ncurses-5.9-10/share/terminfo/2/2621a', dst='/usr/local/share/terminfo/2/2621a', type=3, error=OSError(17, 'File exists'))
[Feb 27 13:44:55] SERR
[Feb 27 13:44:55] SERR
[Feb 27 13:44:55] SOUT
[Feb 27 13:44:55] SOUT Package plan for installation in environment /usr/local:
[Feb 27 13:44:55] SOUT
[Feb 27 13:44:55] SOUT The following packages will be downloaded:
[Feb 27 13:44:55] SOUT
[Feb 27 13:44:55] SOUT package | build
[Feb 27 13:44:55] SOUT ---------------------------|-----------------
[Feb 27 13:44:55] SOUT ca-certificates-2017.1.23 | 0 166 KB conda-forge
[Feb 27 13:44:55] SOUT libgcc-5.2.0 | 0 1.1 MB
[Feb 27 13:44:55] SOUT ncurses-5.9 | 10 1.1 MB conda-forge
[Feb 27 13:44:55] SOUT sqlite-3.13.0 | 1 4.9 MB conda-forge
[Feb 27 13:44:55] SOUT tk-8.5.19 | 1 1.9 MB conda-forge
[Feb 27 13:44:55] SOUT zlib-1.2.11 | 0 93 KB conda-forge
[Feb 27 13:44:55] SOUT openssl-1.0.2h | 3 3.5 MB conda-forge
[Feb 27 13:44:55] SOUT readline-6.2 | 0 713 KB conda-forge
[Feb 27 13:44:55] SOUT curl-7.45.0 | 2 684 KB bioconda
[Feb 27 13:44:55] SOUT python-2.7.12 | 2 13.8 MB conda-forge
[Feb 27 13:44:55] SOUT certifi-2017.1.23 | py27_0 222 KB conda-forge
[Feb 27 13:44:55] SOUT samtools-1.3.1 | 5 874 KB bioconda
[Feb 27 13:44:55] SOUT setuptools-33.1.0 | py27_0 492 KB conda-forge
[Feb 27 13:44:55] SOUT wheel-0.29.0 | py27_0 81 KB conda-forge
[Feb 27 13:44:55] SOUT pip-9.0.1 | py27_0 1.6 MB conda-forge
[Feb 27 13:44:55] SOUT ------------------------------------------------------------
[Feb 27 13:44:55] SOUT Total: 31.1 MB
[Feb 27 13:44:55] SOUT
[Feb 27 13:44:55] SOUT The following NEW packages will be INSTALLED:
[Feb 27 13:44:55] SOUT
[Feb 27 13:44:55] SOUT ca-certificates: 2017.1.23-0 conda-forge (copy)
[Feb 27 13:44:55] SOUT certifi: 2017.1.23-py27_0 conda-forge (copy)
[Feb 27 13:44:55] SOUT curl: 7.45.0-2 bioconda (copy)
[Feb 27 13:44:55] SOUT libgcc: 5.2.0-0 (copy)
[Feb 27 13:44:55] SOUT ncurses: 5.9-10 conda-forge (copy)
[Feb 27 13:44:55] SOUT openssl: 1.0.2h-3 conda-forge (copy)
[Feb 27 13:44:55] SOUT pip: 9.0.1-py27_0 conda-forge (copy)
[Feb 27 13:44:55] SOUT python: 2.7.12-2 conda-forge (copy)
[Feb 27 13:44:55] SOUT readline: 6.2-0 conda-forge (copy)
[Feb 27 13:44:55] SOUT samtools: 1.3.1-5 bioconda (copy)
[Feb 27 13:44:55] SOUT setuptools: 33.1.0-py27_0 conda-forge (copy)
[Feb 27 13:44:55] SOUT sqlite: 3.13.0-1 conda-forge (copy)
[Feb 27 13:44:55] SOUT tk: 8.5.19-1 conda-forge (copy)
[Feb 27 13:44:55] SOUT wheel: 0.29.0-py27_0 conda-forge (copy)
[Feb 27 13:44:55] SOUT zlib: 1.2.11-0 conda-forge (copy)
[Feb 27 13:44:55] SOUT
[Feb 27 13:44:55] ERRO Task processing failed: Unexpected exit code [1] of container [88a2c45c08c6 step-2b07baa1fe], container preserved
Ping @bgruening - any ideas? Should we pin the version of miniconda container we build in?
See galaxyproject/planemo#582 where TravisCI builds are failing planemo conda_init with:
$ planemo conda_init
Traceback (most recent call last):
File "/home/travis/virtualenv/python2.7.9/bin/planemo", line 7, in <module>
from planemo.cli import planemo
File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/planemo/cli.py", line 11, in <module>
from planemo.galaxy import profiles
File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/planemo/galaxy/__init__.py", line 5, in <module>
from .config import galaxy_config
File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/planemo/galaxy/config.py", line 25, in <module>
from planemo.docker import docker_host_args
File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/planemo/docker.py", line 8, in <module>
from galaxy.tools.deps.dockerfiles import docker_host_args
File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/galaxy/tools/deps/dockerfiles.py", line 6, in <module>
from ..deps.containers import docker_cache_path
File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/galaxy/tools/deps/containers.py", line 15, in <module>
from .container_resolvers.explicit import ExplicitContainerResolver
ImportError: No module named container_resolvers.explicit
I've attended the recent @bgruening talk at nf-core hackathon - amazing work of all involved. I can see e.g. multiple containers generated on travis but no luck so far with some of the mulled* tools from this repo. I've tried both conda and pip installation, different virtual environments, python versions but to no avail. Ironically even the associated biocontainer does not play ball.
Is there a fool-proof way of getting this to work on a local (linux) machine?
docker run -it quay.io/biocontainers/galaxy-lib:19.5.2--py_0 mulled-search -s bwa -o biocontainers
Traceback (most recent call last):
File "/usr/local/bin/mulled-search", line 10, in <module>
sys.exit(main())
File "/usr/local/lib/python3.7/site-packages/galaxy/tools/deps/mulled/mulled_search.py", line 126, in main
quay.build_index()
File "/usr/local/lib/python3.7/site-packages/galaxy/tools/deps/mulled/mulled_search.py", line 42, in build_index
r = requests.get(QUAY_API_URL, headers={'Accept-encoding': 'gzip'}, params=parameters,
AttributeError: 'NoneType' object has no attribute 'get'
Hi there!
Is involucro a dependency to galaxy-lib if I want to build containers with it? Is involucro being maintained? Project's last commit seem old. I was going to write a homebrew formula for involucro, but among guidelines for homebrew it says the upstream project needs to be maintained (and last commits seem very old for involucro).
Ping @bgruening
Thanks!
Pablo
Hi there,
I'm trying the mulled-build build-and-test to build a container locally from a conda package through:
mulled-build build-and-test 'r-seurat-workflow=0.0.1--0' --extra-channel file://Users/pmoreno/miniconda3/conda-bld/ --test 'which read-10x.R'
but getting an error:
./involucro -v=2 -f /Users/pmoreno/venvs/mulled/lib/python2.7/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,file://Users/pmoreno/miniconda3/conda-bld/' -set TEST='which read-10x.R' -set TARGETS='r-seurat-workflow=0.0.1=0' -set REPO='quay.io/biocontainers/r-seurat-workflow:0.0.1--0' -set BINDS='build/dist:/usr/local/,/Users/pmoreno/miniconda3/conda-bld/:/Users/pmoreno/miniconda3/conda-bld/' build-and-test
.No handlers could be found for logger "galaxy.tools.deps.commands"
failed MSpanList_Insert 0x878000 0x1f3fa463031a7 0x0 0x0
fatal error: MSpanList_Insert
runtime stack:
runtime.throw(0x584810, 0x10)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/panic.go:530 +0x90 fp=0x7ffeefbff310 sp=0x7ffeefbff2f8
runtime.(*mSpanList).insert(0x7bd888, 0x878000)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:933 +0x293 fp=0x7ffeefbff340 sp=0x7ffeefbff310
runtime.(*mheap).freeSpanLocked(0x7bd080, 0x878000, 0x100, 0x0)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:809 +0x4be fp=0x7ffeefbff3a8 sp=0x7ffeefbff340
runtime.(*mheap).grow(0x7bd080, 0x8, 0x0)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:675 +0x2a0 fp=0x7ffeefbff400 sp=0x7ffeefbff3a8
runtime.(*mheap).allocSpanLocked(0x7bd080, 0x1, 0x0)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:553 +0x4e3 fp=0x7ffeefbff458 sp=0x7ffeefbff400
runtime.(*mheap).alloc_m(0x7bd080, 0x1, 0x15, 0x0)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:437 +0x119 fp=0x7ffeefbff488 sp=0x7ffeefbff458
runtime.(*mheap).alloc.func1()
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:502 +0x41 fp=0x7ffeefbff4b8 sp=0x7ffeefbff488
runtime.systemstack(0x7ffeefbff4d8)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/asm_amd64.s:307 +0xab fp=0x7ffeefbff4c0 sp=0x7ffeefbff4b8
runtime.(*mheap).alloc(0x7bd080, 0x1, 0x10000000015, 0xe9bf)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mheap.go:503 +0x63 fp=0x7ffeefbff508 sp=0x7ffeefbff4c0
runtime.(*mcentral).grow(0x7bec80, 0x0)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mcentral.go:209 +0x93 fp=0x7ffeefbff570 sp=0x7ffeefbff508
runtime.(*mcentral).cacheSpan(0x7bec80, 0x7b7b08)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mcentral.go:89 +0x47d fp=0x7ffeefbff5b0 sp=0x7ffeefbff570
runtime.(*mcache).refill(0x874000, 0x15, 0x7ffeefbff618)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/mcache.go:119 +0xcc fp=0x7ffeefbff5e8 sp=0x7ffeefbff5b0
runtime.mallocgc.func2()
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/malloc.go:642 +0x2b fp=0x7ffeefbff608 sp=0x7ffeefbff5e8
runtime.systemstack(0x7ffeefbff6a8)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/asm_amd64.s:307 +0xab fp=0x7ffeefbff610 sp=0x7ffeefbff608
runtime.mallocgc(0x180, 0x521e60, 0x0, 0x800000000)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/malloc.go:643 +0x869 fp=0x7ffeefbff6e8 sp=0x7ffeefbff610
runtime.newobject(0x521e60, 0x7b7fb0)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/malloc.go:781 +0x42 fp=0x7ffeefbff710 sp=0x7ffeefbff6e8
runtime.malg(0x8000, 0x7b8360)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/proc.go:2634 +0x27 fp=0x7ffeefbff748 sp=0x7ffeefbff710
runtime.mpreinit(0x7b8900)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/os1_darwin.go:140 +0x1f fp=0x7ffeefbff760 sp=0x7ffeefbff748
runtime.mcommoninit(0x7b8900)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/proc.go:494 +0x105 fp=0x7ffeefbff7a8 sp=0x7ffeefbff760
runtime.schedinit()
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/proc.go:434 +0x79 fp=0x7ffeefbff7f0 sp=0x7ffeefbff7a8
runtime.rt0_go(0x7ffeefbff820, 0xf, 0x7ffeefbff820, 0x0, 0xf, 0x7ffeefbff9b8, 0x7ffeefbff9c4, 0x7ffeefbff9c9, 0x7ffeefbff9cc, 0x7ffeefbffa29, ...)
/Users/travis/.gimme/versions/go1.6.darwin.amd64/src/runtime/asm_amd64.s:138 +0x132 fp=0x7ffeefbff7f8 sp=0x7ffeefbff7f0
This was both using the staticly built involucro that I manually downloaded from the releases on github or relying on the auto download (removing my binary from the path). Should I be trying to build involucro locally?
Before trying this I conda built my package locally succesfully (and indexed my local lib). I installed galaxy-lib through pip install galaxy-lib.
Any ideas @bgruening?
Thanks!
Hi all,
I'm interested in using the local generation of container from bioconda packages for packages that we have in development (so that we can have a container way sooner than the package is actually accepted in conda). I'm concerned though about the strong coupling/vendor lock-in with quay.io. Would it be possible for the mulled/involucro script to leave the docker image available locally so that it can be pushed "manually" or independently to other registries that are not quay.io? I can put sometime on this, but I need to understand how constrained we are by how involucro works.
Thanks!
In a recent (?) release of this library, new imports were added to util/path/init.py that are problematic on Windows. The galaxy-lib module is used by pulsar on Windows, and these imports force an unhandled exception. The problematic imports are:
from grp import getgrpid
and
from pwd import getpwuid
Commenting these out restores pulsar functionality.
These could by masked by a try/except ImportError/pass block.
Thanks,
It would be nice to have something like
mulled run bwa==0.14 samtools==1.2 -- bwa mem ...
This makes a lot of sense to me - it'd be a much nicer endpoint for new CLI users.
[ 60s] FAIL: Doctest: galaxy.util.size_to_bytes
[ 60s] ----------------------------------------------------------------------
[ 60s] Traceback (most recent call last):
[ 60s] File "/usr/lib/python2.7/doctest.py", line 2224, in runTest
[ 60s] raise self.failureException(self.format_failure(new.getvalue()))
[ 60s] AssertionError: Failed doctest test for galaxy.util.size_to_bytes
[ 60s] File "/home/abuild/rpmbuild/BUILD/galaxy-lib-19.5.2/galaxy/util/__init__.py", line 1360, in size_to_bytes
[ 60s]
[ 60s] ----------------------------------------------------------------------
[ 60s] File "/home/abuild/rpmbuild/BUILD/galaxy-lib-19.5.2/galaxy/util/__init__.py", line 1372, in galaxy.util.size_to_bytes
[ 60s] Failed example:
[ 60s] size_to_bytes('2.2 TB')
[ 60s] Expected:
[ 60s] 2418925581107
[ 60s] Got:
[ 60s] 2418925581107L
[ 60s] ----------------------------------------------------------------------
[ 60s] File "/home/abuild/rpmbuild/BUILD/galaxy-lib-19.5.2/galaxy/util/__init__.py", line 1374, in galaxy.util.size_to_bytes
[ 60s] Failed example:
[ 60s] size_to_bytes('.01 TB')
[ 60s] Expected:
[ 60s] 10995116277
[ 60s] Got:
[ 60s] 10995116277L
[ 60s]
[ 60s] >> raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0xb634eb8c>.getvalue()))mulled is too susceptible to unforeseen changes in the continuumio/miniconda3 images by using the latest tag. See bioconda/bioconda-recipes#8044 (comment):
The build failure is due to
mulledpullingcontinuumio/miniconda3:latestwhich, unfortunately, has been updated to4.4.10: https://hub.docker.com/r/continuumio/miniconda/tags/. That caused themulledbuild to run into conda/conda#6811
What about adding https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tools/xsd/ in galaxy/tools/ ? Then we can remove planemo/xml/xsd/tool/galaxy.xsd from planemo.
Just a minor issue, but the Documentation link to readthedocs is empty (just click it on the main README page).
When trying to build with mulled on Ubuntu 16.04, the process fails at the container creation level due to not finding the local packages. Local packages are found correctly by conda before involucro, but involucro process seems to miss the packages. Steps executed are the following:
# after checking out https://github.com/ebi-gene-expression-group/bioconda-recipes
# and switching to the r-seurat-workflow branch
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda build recipes/r-seurat-scripts
conda index /miniconda/conda-bld/linux64/
mulled-build build-and-test 'r-seurat-scripts=0.0.1--0' \
--extra-channel file://miniconda/conda-bld/ --test 'which read-10x.R' \
--namespace ebigxa \
--oauth-token <our-token> \
--involucro-path /usr/local/go/bin/involucro
Output with error is:
+ conda config --add channels r
+ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
+ conda config --add channels conda-forge
+ conda config --add channels bioconda
+ conda build recipes/r-seurat-scripts
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-seurat-scripts
INFO:conda_build.metadata:Attempting to finalize metadata for r-seurat-scripts
Solving environment: ...working... done
Solving environment: ...working... done
BUILD START: ['r-seurat-scripts-0.0.1-0.tar.bz2']
Solving environment: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /miniconda/conda-bld/r-seurat-scripts_1530872875082/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
The following NEW packages will be INSTALLED:
ca-certificates: 2018.4.16-0 conda-forge
curl: 7.60.0-0 conda-forge
expat: 2.2.5-hfc679d8_1 conda-forge
gettext: 0.19.8.1-0 conda-forge
git: 2.18.0-pl526hbb17d3c_1 conda-forge
krb5: 1.14.6-0 conda-forge
libgcc-ng: 7.2.0-hdf63c60_3
libiconv: 1.15-h470a237_1 conda-forge
libssh2: 1.8.0-h5b517e9_2 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3
openssl: 1.0.2o-0 conda-forge
perl: 5.26.2-h14c3975_0
tk: 8.6.7-0 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Cloning into bare repository '/miniconda/conda-bld/git_cache/github.com/ebi-gene-expression-group/r-seurat-scripts.git'...
Cloning into '/miniconda/conda-bld/r-seurat-scripts_1530872875082/work'...
done.
Your branch is up to date with 'origin/master'.
fatal: No names found, cannot describe anything.
commit 3edb11c3b6435d19efa9a1e3a235e19ac8a5cc34
Author: Jonathan Manning <[email protected]>
Date: Fri Jul 6 11:07:54 2018 +0100
Updated README
commit 3edb11c3b6435d19efa9a1e3a235e19ac8a5cc34
Author: Jonathan Manning <[email protected]>
Date: Fri Jul 6 11:07:54 2018 +0100
Updated README
On branch master
Your branch is up to date with 'origin/master'.
nothing to commit, working tree clean
checkout: 'HEAD'
==> git log -n1 <==
==> git describe --tags --dirty <==
==> git status <==
source tree in: /miniconda/conda-bld/r-seurat-scripts_1530872875082/work
Resource usage statistics from building r-seurat-scripts:
Process count: 1
CPU time: unavailable
Memory: 3.2M
Disk usage: 804B
Time elapsed: 0:00:02.1
Packaging r-seurat-scripts
INFO:conda_build.build:Packaging r-seurat-scripts
Packaging r-seurat-scripts-0.0.1-0
INFO:conda_build.build:Packaging r-seurat-scripts-0.0.1-0
fatal: No names found, cannot describe anything.
number of files: 8
Fixing permissions
Detected hard-coded path in text file bin/conda_build.sh
updating: r-seurat-scripts-0.0.1-0.tar.bz2
TEST START: /miniconda/conda-bld/linux-64/r-seurat-scripts-0.0.1-0.tar.bz2
Updating index at /miniconda/conda-bld/linux-64 to make package installable with dependencies
INFO:conda_build.build:Updating index at /miniconda/conda-bld/linux-64 to make package installable with dependencies
Updating index at /miniconda/conda-bld/noarch to make package installable with dependencies
INFO:conda_build.build:Updating index at /miniconda/conda-bld/noarch to make package installable with dependencies
Adding in variants from /tmp/tmpz3lo7hf7/info/recipe/conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /tmp/tmpz3lo7hf7/info/recipe/conda_build_config.yaml
Renaming work directory, /miniconda/conda-bld/r-seurat-scripts_1530872875082/work to /miniconda/conda-bld/r-seurat-scripts_1530872875082/work_moved_r-seurat-scripts-0.0.1-0_linux-64
Solving environment: ...working... done
## Package Plan ##
environment location: /miniconda/conda-bld/r-seurat-scripts_1530872875082/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
The following NEW packages will be INSTALLED:
bzip2: 1.0.6-1 conda-forge
ca-certificates: 2018.4.16-0 conda-forge
cairo: 1.14.12-he56eebe_0 conda-forge
curl: 7.60.0-0 conda-forge
fontconfig: 2.13.0-1 conda-forge
freetype: 2.8.1-0 conda-forge
gettext: 0.19.8.1-0 conda-forge
glib: 2.55.0-0 conda-forge
gmp: 6.1.2-hfc679d8_0 conda-forge
graphite2: 1.3.11-hfc679d8_0 conda-forge
gsl: 2.1-2 conda-forge
harfbuzz: 1.7.6-0 conda-forge
icu: 58.2-hfc679d8_0 conda-forge
jpeg: 9c-h470a237_0 conda-forge
krb5: 1.14.6-0 conda-forge
libffi: 3.2.1-3 conda-forge
libgcc: 7.2.0-h69d50b8_2
libgcc-ng: 7.2.0-hdf63c60_3
libiconv: 1.15-h470a237_1 conda-forge
libpng: 1.6.34-ha92aebf_1 conda-forge
libssh2: 1.8.0-h5b517e9_2 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3
libtiff: 4.0.9-he6b73bb_1 conda-forge
libuuid: 1.0.3-1 conda-forge
libxcb: 1.13-h470a237_0 conda-forge
libxml2: 2.9.8-h422b904_1 conda-forge
ncurses: 5.9-10 conda-forge
openjdk: 8.0.121-1
openssl: 1.0.2o-0 conda-forge
pango: 1.40.14-hd50be51_1 conda-forge
pcre: 8.39-0 conda-forge
pixman: 0.34.0-2 conda-forge
r-abind: 1.4_5-r3.4.1_0 conda-forge
r-acepack: 1.4.1-r3.4.1_0 conda-forge
r-ape: 5.1-r3.4.1_0 conda-forge
r-assertthat: 0.2.0-r3.4.1_0 conda-forge
r-backports: 1.1.2-r3.4.1_0 conda-forge
r-base: 3.4.1-4 conda-forge
r-base64enc: 0.1_3-r3.4.1_0 conda-forge
r-bh: 1.66.0_1-r3.4.1_0 conda-forge
r-bindr: 0.1.1-r3.4.1_0 conda-forge
r-bindrcpp: 0.2-r3.4.1_0 conda-forge
r-bitops: 1.0_6-r3.4.1_0 conda-forge
r-broom: 0.4.4-r3.4.1_0 conda-forge
r-caret: 6.0_79-r3.4.1_0 conda-forge
r-catools: 1.17.1-r3.4.1_0 conda-forge
r-checkmate: 1.8.5-r3.4.1_0 conda-forge
r-class: 7.3_14-r3.4.1_0 conda-forge
r-cli: 1.0.0-r3.4.1_0 conda-forge
r-cluster: 2.0.6-r3.4.1_0 conda-forge
r-codetools: 0.2_15-r3.4.1_0 conda-forge
r-colorspace: 1.3_2-r3.4.1_0 conda-forge
r-cowplot: 0.9.2-r3.4.1_0 conda-forge
r-crayon: 1.3.4-r3.4.1_0 conda-forge
r-crosstalk: 1.0.0-r3.4.1_0 conda-forge
r-curl: 3.2-r3.4.1_0 conda-forge
r-cvst: 0.2_1-r3.4.1_0 conda-forge
r-data.table: 1.10.4-r3.4.1_0 bioconda
r-ddalpha: 1.3.4-r341_0 conda-forge
r-deoptimr: 1.0_8-r3.4.1_0 bioconda
r-devtools: 1.13.6-r341_0 conda-forge
r-dichromat: 2.0_0-r3.4.1_0 conda-forge
r-diffusionmap: 1.1_0-r3.4.1_0 conda-forge
r-digest: 0.6.15-r3.4.1_0 conda-forge
r-dimred: 0.1.0-r3.4.1_0 conda-forge
r-diptest: 0.75_7-r3.4.1_0 bioconda
r-doparallel: 1.0.11-r3.4.1_0 conda-forge
r-dosnow: 1.0.16-r3.4.1_0 conda-forge
r-dplyr: 0.7.4-r3.4.1_0 conda-forge
r-drr: 0.0.3-r3.4.1_0 conda-forge
r-dtw: 1.18_1-r3.4.1_0 conda-forge
r-evaluate: 0.10.1-r3.4.1_0 conda-forge
r-fitdistrplus: 1.0_9-r3.4.1_0 conda-forge
r-flexmix: 2.3_14-r3.4.1_0 conda-forge
r-fnn: 1.1-r3.4.1_0 bioconda
r-foreach: 1.4.4-r3.4.1_0 conda-forge
r-foreign: 0.8_67-r3.4.1_0 conda-forge
r-formula: 1.2_1-r3.4.1_0 conda-forge
r-fpc: 2.1_10-r3.4.1_0 conda-forge
r-gdata: 2.18.0-r3.4.1_0 conda-forge
r-geometry: 0.3_6-r3.4.1_0 conda-forge
r-getopt: 1.20.2-r3.4.1_0 conda-forge
r-ggplot2: 2.2.1-r3.4.1_0 conda-forge
r-ggridges: 0.5.0-r3.4.1_0 conda-forge
r-git2r: 0.21.0-r341h0c37787_0 conda-forge
r-glue: 1.2.0-r3.4.1_0 conda-forge
r-gower: 0.1.2-r3.4.1_0 conda-forge
r-gplots: 3.0.1-r3.4.1_0 conda-forge
r-gridbase: 0.4_7-r3.4.1_0 conda-forge
r-gridextra: 2.3-r3.4.1_0 conda-forge
r-gtable: 0.2.0-r3.4.1_0 conda-forge
r-gtools: 3.8.1-r341_0 conda-forge
r-hexbin: 1.27.2-r3.4.1_0 conda-forge
r-highr: 0.7-r341_0 conda-forge
r-hmisc: 4.0_3-r3.4.1_0 conda-forge
r-htmltable: 1.9-r3.4.1_0 conda-forge
r-htmltools: 0.3.6-r3.4.1_0 conda-forge
r-htmlwidgets: 1.0-r3.4.1_0 conda-forge
r-httpuv: 1.3.6.2-r3.4.1_0 conda-forge
r-httr: 1.3.1-r3.4.1_0 conda-forge
r-ica: 1.0_1-r3.4.1_0 conda-forge
r-igraph: 1.2.1-r3.4.1_0 conda-forge
r-ipred: 0.9_6-r3.4.1_0 conda-forge
r-irlba: 2.3.2-r3.4.1_0 conda-forge
r-iterators: 1.0.9-r3.4.1_0 conda-forge
r-jsonlite: 1.5-r3.4.1_0 conda-forge
r-kernlab: 0.9_25-r3.4.1_0 conda-forge
r-kernsmooth: 2.23_15-r3.4.1_0 conda-forge
r-knitr: 1.20-r3.4.1_0 conda-forge
r-labeling: 0.3-r3.4.1_0 conda-forge
r-lars: 1.2-r3.4.1_0 conda-forge
r-lattice: 0.20_34-r3.4.1_0 conda-forge
r-latticeextra: 0.6_28-r3.4.1_0 conda-forge
r-lava: 1.6.1-r3.4.1_0 conda-forge
r-lazyeval: 0.2.1-r3.4.1_0 conda-forge
r-lmtest: 0.9_35-r3.4.1_0 conda-forge
r-lubridate: 1.7.4-r3.4.1_0 conda-forge
r-magic: 1.5_6-r3.4.1_0 conda-forge
r-magrittr: 1.5-r3.4.1_0 conda-forge
r-markdown: 0.8-r3.4.1_1 conda-forge
r-mass: 7.3_48-r3.4.1_0 conda-forge
r-matrix: 1.2_14-r3.4.1_0 conda-forge
r-mclust: 5.4.1-r341_0 conda-forge
r-memoise: 1.1.0-r3.4.1_0 conda-forge
r-metap: 0.8-r3.4.1_0 conda-forge
r-mime: 0.5-r3.4.1_0 conda-forge
r-mixtools: 1.1.0-r3.4.1_0 conda-forge
r-mnormt: 1.5_5-r3.4.1_0 conda-forge
r-modelmetrics: 1.1.0-r3.4.1_0 conda-forge
r-modeltools: 0.2_21-r3.4.1_0 conda-forge
r-munsell: 0.5.0-r341_0 conda-forge
r-mvtnorm: 1.0_6-r3.4.1_0 conda-forge
r-nlme: 3.1_131-r3.4.1_0 conda-forge
r-nmf: 0.21.0-r3.4.1_0 conda-forge
r-nnet: 7.3_12-r3.4.1_0 conda-forge
r-numderiv: 2016.8_1-r3.4.1_0 conda-forge
r-openssl: 1.0.1-r3.4.1_0 conda-forge
r-optparse: 1.6.0-r341_0 conda-forge
r-pbapply: 1.3_3-r3.4.1_0 conda-forge
r-pillar: 1.2.2-r341h6115d3f_1 conda-forge
r-pkgconfig: 2.0.1-r3.4.1_0 conda-forge
r-pkgmaker: 0.22-r3.4.1_0 conda-forge
r-plogr: 0.1_1-r3.4.1_0 conda-forge
r-plotly: 4.7.1-r3.4.1_0 conda-forge
r-pls: 2.6_0-r3.4.1_0 conda-forge
r-plyr: 1.8.4-r3.4.1_0 conda-forge
r-png: 0.1_7-r3.4.1_0 conda-forge
r-prabclus: 2.2_6-r3.4.1_0 conda-forge
r-prodlim: 2018.04.18-r3.4.1_0 conda-forge
r-proxy: 0.4_17-r3.4.1_0 conda-forge
r-psych: 1.5.8-r3.4.1_0 bioconda
r-purrr: 0.2.4-r3.4.1_0 conda-forge
r-r.methodss3: 1.7.1-r3.4.1_0 conda-forge
r-r.oo: 1.21.0-r3.4.1_0 conda-forge
r-r.utils: 2.6.0-r3.4.1_0 conda-forge
r-r6: 2.2.2-r3.4.1_0 conda-forge
r-ranger: 0.10.1-r341_0 conda-forge
r-rann: 2.5.1-r3.4.1_0 conda-forge
r-rcolorbrewer: 1.1_2-r3.4.1_0 conda-forge
r-rcpp: 0.12.15-r3.4.1_0 conda-forge
r-rcppeigen: 0.3.3.4.0-r3.4.1_0 conda-forge
r-rcppprogress: 0.4-r3.4.1_0 conda-forge
r-rcpproll: 0.2.2-r3.4.1_0 conda-forge
r-recipes: 0.1.3-r341_0 conda-forge
r-registry: 0.5-r3.4.1_0 conda-forge
r-reshape2: 1.4.3-r3.4.1_0 conda-forge
r-reticulate: 1.8-r341_0 conda-forge
r-rlang: 0.2.1-r341_0 conda-forge
r-rngtools: 1.3.1-r341_0 conda-forge
r-robustbase: 0.92_7-r3.4.1_0 conda-forge
r-rocr: 1.0_7-r3.4.1_0 conda-forge
r-rpart: 4.1_13-r3.4.1_0 conda-forge
r-rstudioapi: 0.7-r3.4.1_0 conda-forge
r-rtsne: 0.13-r3.4.1_0 conda-forge
r-scales: 0.5.0-r3.4.1_0 conda-forge
r-scatterplot3d: 0.3_40-r3.4.1_0 conda-forge
r-sdmtools: 1.1_221-r3.4.1_1 conda-forge
r-segmented: 0.5_2.1-r3.4.1_0 conda-forge
r-seurat: 2.3.1-r3.4.1_0 bioconda
r-seurat-scripts: 0.0.1-0 local
r-sfsmisc: 1.1_1-r3.4.1_0 conda-forge
r-shiny: 1.0.5-r3.4.1_0 conda-forge
r-sn: 1.5_0-r3.4.1_0 conda-forge
r-snow: 0.4_2-r3.4.1_0 conda-forge
r-sourcetools: 0.1.6-r3.4.1_0 conda-forge
r-squarem: 2017.10_1-r3.4.1_0 conda-forge
r-stringi: 1.1.7-r3.4.1_1 conda-forge
r-stringr: 1.3.0-r3.4.1_0 conda-forge
r-survival: 2.40_1-r3.4.1_0 conda-forge
r-tclust: 1.3_1-r3.4.1_0 conda-forge
r-tibble: 1.4.2-r3.4.1_0 conda-forge
r-tidyr: 0.8.1-r341_0 conda-forge
r-tidyselect: 0.2.4-r3.4.1_0 conda-forge
r-timedate: 3012.100-r3.4.1_0 conda-forge
r-trimcluster: 0.1_2-r3.4.1_0 conda-forge
r-tsne: 0.1_3-r3.4.1_0 conda-forge
r-utf8: 1.1.3-r3.4.1_0 conda-forge
r-vgam: 1.0_3-r3.4.1_0 conda-forge
r-viridis: 0.5.1-r3.4.1_0 conda-forge
r-viridislite: 0.3.0-r3.4.1_0 conda-forge
r-whisker: 0.3_2-r3.4.1_0 conda-forge
r-withr: 2.1.1-r3.4.1_0 conda-forge
r-xtable: 1.8_2-r3.4.1_0 conda-forge
r-yaml: 2.1.18-r3.4.1_0 conda-forge
r-zoo: 1.8_1-r3.4.1_0 conda-forge
readline: 7.0-0 conda-forge
tk: 8.6.7-0 conda-forge
xorg-kbproto: 1.0.7-h470a237_2 conda-forge
xorg-libice: 1.0.9-2 conda-forge
xorg-libsm: 1.2.2-2 conda-forge
xorg-libx11: 1.6.5-0 conda-forge
xorg-libxau: 1.0.8-h470a237_4 conda-forge
xorg-libxdmcp: 1.1.2-h470a237_4 conda-forge
xorg-libxrender: 0.9.10-0 conda-forge
xorg-renderproto: 0.11.1-h470a237_2 conda-forge
xorg-xproto: 7.0.31-h470a237_7 conda-forge
xz: 5.2.3-0 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ which read-10x.R
/miniconda/conda-bld/r-seurat-scripts_1530872875082/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/read-10x.R
+ which create-seurat-object.R
/miniconda/conda-bld/r-seurat-scripts_1530872875082/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/create-seurat-object.R
+ exit 0
Resource usage statistics from testing r-seurat-scripts:
Process count: 1
CPU time: Sys=0:00:00.0, User=0:00:00.0
Memory: 2.9M
Disk usage: 12B
Time elapsed: 0:00:02.0
TEST END: /miniconda/conda-bld/linux-64/r-seurat-scripts-0.0.1-0.tar.bz2
Renaming work directory, /miniconda/conda-bld/r-seurat-scripts_1530872875082/work to /miniconda/conda-bld/r-seurat-scripts_1530872875082/work_moved_r-seurat-scripts-0.0.1-0_linux-64_main_build_loop
# Automatic uploading is disabled
# If you want to upload package(s) to anaconda.org later, type:
anaconda upload /miniconda/conda-bld/linux-64/r-seurat-scripts-0.0.1-0.tar.bz2
# To have conda build upload to anaconda.org automatically, use
# $ conda config --set anaconda_upload yes
anaconda_upload is not set. Not uploading wheels: []
####################################################################################
Resource usage summary:
Total time: 0:14:06.2
CPU usage: sys=0:00:00.0, user=0:00:00.0
Maximum memory usage observed: 3.2M
Total disk usage observed (not including envs): 816B
####################################################################################
Source and build intermediates have been left in /miniconda/conda-bld.
There are currently 2 accumulated.
To remove them, you can run the ```conda build purge``` command
+ conda index /miniconda/conda-bld/linux64/
+ mulled-build build-and-test r-seurat-scripts=0.0.1--0 --extra-channel file://miniconda/conda-bld/ --test which read-10x.R --namespace ebigxa --oauth-token <our-token> --involucro-path /usr/local/go/bin/involucro
/usr/local/go/bin/involucro -v=2 -f /miniconda/lib/python3.6/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,file://miniconda/conda-bld/' -set TEST='which read-10x.R' -set TARGETS='r-seurat-scripts=0.0.1=0' -set REPO='quay.io/ebigxa/r-seurat-scripts:0.0.1--0' -set BINDS='build/dist:/usr/local/,/miniconda/conda-bld/:/miniconda/conda-bld/' build-and-test
.Passing program arguments as a string may be a security hazard if combined with untrusted input
[Jul 6 10:42:03] DEBU Run file [/miniconda/lib/python3.6/site-packages/galaxy/tools/deps/mulled/invfile.lua]
[Jul 6 10:42:03] INFO Invoke Task [build]
[Jul 6 10:42:03] STEP Run image [continuumio/miniconda3:latest] with command [[rm -rf /data/dist]]
[Jul 6 10:42:03] DEBU Creating container [step-179d88c583]
[Jul 6 10:42:03] DEBU Image [continuumio/miniconda3:latest] not present, pulling it
[Jul 6 10:42:03] DEBU Pull Image [continuumio/miniconda3:latest]
[Jul 6 10:42:16] DEBU Created container [891cd94c48c4 step-179d88c583], starting it
[Jul 6 10:42:17] DEBU Container [891cd94c48c4 step-179d88c583] started, waiting for completion
[Jul 6 10:42:17] DEBU Container [891cd94c48c4 step-179d88c583] completed with exit code [0] as expected
[Jul 6 10:42:17] DEBU Container [891cd94c48c4 step-179d88c583] removed
[Jul 6 10:42:17] STEP Run image [continuumio/miniconda3:latest] with command [[/bin/sh -c conda install -c bioconda -c file://miniconda/conda-bld/ r-seurat-scripts=0.0.1=0 -p /usr/local --copy --yes --quiet]]
[Jul 6 10:42:17] DEBU Creating container [step-15063d3438]
[Jul 6 10:42:18] DEBU Created container [c7d0befe7e20 step-15063d3438], starting it
[Jul 6 10:42:18] DEBU Container [c7d0befe7e20 step-15063d3438] started, waiting for completion
[Jul 6 10:42:31] SOUT Solving environment: ...working... failed
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR PackagesNotFoundError: The following packages are not available from current channels:
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-cowplot
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-pbapply
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-ranger
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-rcppprogress
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-tclust
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-diffusionmap
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-dtw
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-ggridges
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-ica
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-sdmtools
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-dosnow
[Jul 6 10:42:31] SERR - r-seurat-scripts==0.0.1=0
[Jul 6 10:42:31] SERR - r-seurat
[Jul 6 10:42:31] SERR - r-metap
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR Current channels:
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR - https://conda.anaconda.org/bioconda/linux-64
[Jul 6 10:42:31] SERR - https://conda.anaconda.org/bioconda/noarch
[Jul 6 10:42:31] SERR - file://miniconda/conda-bld/linux-64
[Jul 6 10:42:31] SERR - file://miniconda/conda-bld/noarch
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/main/linux-64
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/main/noarch
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/free/linux-64
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/free/noarch
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/r/linux-64
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/r/noarch
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/pro/linux-64
[Jul 6 10:42:31] SERR - https://repo.anaconda.com/pkgs/pro/noarch
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR To search for alternate channels that may provide the conda package you're
[Jul 6 10:42:31] SERR looking for, navigate to
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR https://anaconda.org
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR and use the search bar at the top of the page.
[Jul 6 10:42:31] SERR
[Jul 6 10:42:31] SERR
[Jul 6 10:42:32] ERRO Task processing failed: Unexpected exit code [1] of container [c7d0befe7e20 step-15063d3438], container preserved
We've made a decision to heard developers into a fixed set of "best practice" channels, I think it has been a fine choice. As a result the mulled hash that maps package lists to containers doesn't allow specifying channels (they are assumed to be the "best practice" channels). But other prominent platforms give developers the option to select channels when defining tools / workflows:
This is a not the route we took, but it would be nice if the the plumbing we developed would work with such specifications - the mulled-* tools, galaxy-lib dependency and container resolution, multi-package-containers, planemo-monitor, etc... One can imagine a new mulled hash that also incorporated the list of channels in the computation would be all that would needed here right?
I think making our tooling and such compatible with these other platforms is a good goal in its own right, but it might also help current supported tool formats also? I'm not sure I'd want to fight to expose this functionality in Galaxy tools, but for CWL resolution - it would be nice to have a modality that matched the Snakemake / Nextflow paradigm (in addition to the Galaxy paradigm already supported by cwltool and Toil).
mulled always downloads involucro unless it is in the current working directory or --involucro-path is provided. It fails to detect if involucro is available via PATH since https://github.com/galaxyproject/galaxy-lib/blob/18.5.7/galaxy/tools/deps/mulled/mulled_build.py#L288 does not inspect PATH.
In Python >=3.3 this could be solved by using shutil.which.
For Python 2 compatibility, there are some packages, e.g., backports.shutil_which or whichcraft, that backport the functionality from https://github.com/python/cpython/blob/3.7/Lib/shutil.py#L1109-L1169.
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