Re: [galaxy-dev] conversion issue

8 Aug 2016

      I tried to reinstall some tools, but I still get an error message:

Fatal error: Exit code 1 ()
bedtools: /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by bedtools)
needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
Traceback (most recent call last):
  File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 122, in <module>
    main(*args, **kwargs)
  File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 57, in main
    convert_to_bigwig(temp_file, sizes, config, outfile)
  File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 104, in convert_to_bigwig
    subprocess.check_call(cl)
  File "/galaxy-central/tool_deps/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bedGraphToBigWig', '/tmp/tmpkiKe2V', '/export/galaxy-central/database/files/003/dataset_3153-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3153.dat']' returned non-zero exit status 255

It seems Bedrolls requires 

GLIBCXX_3.4.15

Since I am using Galaxy-docker I am not sure how to get this installed...

Always grateful for help.

Cheers,

Philipp

-----Original message-----
From: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>
Sent: Friday 5th August 2016 16:26
To: Peter Cock <p.j.a.cock@googlemail.com>
Cc: Brad Chapman <chapmanb@50mail.com>; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] conversion issue

Hi Peter,

it looks like samtools is not functional....

==> /home/galaxy/logs/uwsgi.log <==

galaxy.tools DEBUG 2016-08-05 14:25:25,686 Validated and populated state for tool request (52.679 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,754 Handled output named out for tool toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 (26.340 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,767 Added output datasets to history (13.170 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,793 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] (11.785 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,794 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] complete, ready to flush (26.847 ms)

galaxy.tools.actions INFO 2016-08-05 14:25:25,841 Flushed transaction for job Job[id=2438,tool_id=toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] (47.380 ms)

galaxy.tools.execute DEBUG 2016-08-05 14:25:25,842 Tool [toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0] created job [2438] (130.941 ms)

galaxy.tools.execute DEBUG 2016-08-05 14:25:25,851 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.2.0 request: (164.591 ms)

172.17.0.1 - - [05/Aug/2016:14:25:25 +0000] "POST /api/tools HTTP/1.1" 200 - "http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 381|app: 0|req: 53/85] 172.17.0.1 () {52 vars in 973 bytes} [Fri Aug  5 14:25:25 2016] POST /api/tools => generated 983 bytes in 256 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)

172.17.0.1 - - [05/Aug/2016:14:25:25 +0000] "GET /api/histories/b701da857886499b/contents?v=dev HTTP/1.1" 200 - "http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

[pid: 382|app: 0|req: 33/86] 172.17.0.1 () {46 vars in 921 bytes} [Fri Aug  5 14:25:25 2016] GET /api/histories/b701da857886499b/contents?v=dev => generated 125847 bytes in 127 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2)

==> /home/galaxy/logs/handler0.log <==

galaxy.jobs DEBUG 2016-08-05 14:25:26,391 (2438) Working directory for job is: /export/galaxy-central/database/job_working_directory/002/2438

galaxy.jobs.handler DEBUG 2016-08-05 14:25:26,401 (2438) Dispatching to slurm runner

galaxy.jobs DEBUG 2016-08-05 14:25:26,436 (2438) Persisting job destination (destination id: slurm_cluster)

galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,450 Job [2438] queued (48.081 ms)

galaxy.jobs.handler INFO 2016-08-05 14:25:26,457 (2438) Job dispatched

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Building dependency shell command for dependency 'pysam'

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,693 Find dependency pysam version 0.8.3

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fb0dd3b7f50> (isnull? False)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Building dependency shell command for dependency 'bedtools'

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,700 Find dependency bedtools version 2.24

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,702 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fb0dc496ed0> (isnull? False)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,702 Building dependency shell command for dependency 'ucsc_tools'

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,702 Find dependency ucsc_tools version 312

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,705 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fb0dd3b7f50> (isnull? False)

galaxy.jobs.command_factory INFO 2016-08-05 14:25:26,737 Built script [/export/galaxy-central/database/job_working_directory/002/2438/tool_script.sh] for tool command[PACKAGE_BASE=/galaxy-central/tool_deps/pysam/0.8.3/brad-chapman/bam_to_bigwig/9163e1db4c16; export PACKAGE_BASE; . /galaxy-central/tool_deps/pysam/0.8.3/brad-chapman/bam_to_bigwig/9163e1db4c16/env.sh; PACKAGE_BASE=/galaxy-central/tool_deps/bedtools/2.24/brad-chapman/bam_to_bigwig/9163e1db4c16; export PACKAGE_BASE; . /galaxy-central/tool_deps/bedtools/2.24/brad-chapman/bam_to_bigwig/9163e1db4c16/env.sh; PACKAGE_BASE=/galaxy-central/tool_deps/ucsc_tools/312/brad-chapman/bam_to_bigwig/9163e1db4c16; export PACKAGE_BASE; . /galaxy-central/tool_deps/ucsc_tools/312/brad-chapman/bam_to_bigwig/9163e1db4c16/env.sh; python /shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py /export/galaxy-central/database/files/003/dataset_3088.dat --outfile=/export/galaxy-central/database/files/003/dataset_3117.dat --split]

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,884 Building dependency shell command for dependency 'samtools'

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,884 Find dependency samtools version None

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,885 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,885 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,886 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,886 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True)

galaxy.tools.deps DEBUG 2016-08-05 14:25:26,887 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7fb0ea2c3dd0> (isnull? True)

galaxy.tools.deps WARNING 2016-08-05 14:25:26,887 Failed to resolve dependency on 'samtools', ignoring

galaxy.jobs.runners DEBUG 2016-08-05 14:25:26,907 (2438) command is: mkdir -p working; cd working; /export/galaxy-central/database/job_working_directory/002/2438/tool_script.sh; return_code=$?; cd '/export/galaxy-central/database/job_working_directory/002/2438'; python "/export/galaxy-central/database/job_working_directory/002/2438/set_metadata_hmqtZc.py" "/export/galaxy-central/database/files/tmpBPe1aw" "/export/galaxy-central/database/job_working_directory/002/2438/working/galaxy.json" "/export/galaxy-central/database/job_working_directory/002/2438/metadata_in_HistoryDatasetAssociation_3277_AUIB9T,/export/galaxy-central/database/job_working_directory/002/2438/metadata_kwds_HistoryDatasetAssociation_3277_5_v2O7,/export/galaxy-central/database/job_working_directory/002/2438/metadata_out_HistoryDatasetAssociation_3277_96qP8H,/export/galaxy-central/database/job_working_directory/002/2438/metadata_results_HistoryDatasetAssociation_3277_mCFIaX,/export/galaxy-central/database/files/003/dataset_3117.dat,/export/galaxy-central/database/job_working_directory/002/2438/metadata_override_HistoryDatasetAssociation_3277_Fi9GIQ" 5242880; sh -c "exit $return_code"

galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:26,936 (2438) submitting file /export/galaxy-central/database/job_working_directory/002/2438/galaxy_2438.sh

galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:26,937 (2438) native specification is: --ntasks=1 --share

galaxy.jobs.runners.drmaa INFO 2016-08-05 14:25:26,938 (2438) queued as 7

galaxy.jobs DEBUG 2016-08-05 14:25:26,938 (2438) Persisting job destination (destination id: slurm_cluster)

==> /home/galaxy/logs/slurmctld.log <==

[2016-08-05T14:25:26.938] _slurm_rpc_submit_batch_job JobId=7 usec=251

[2016-08-05T14:25:26.941] sched: Allocate JobId=7 NodeList=5e2648045373 #CPUs=1

==> /home/galaxy/logs/slurmd.log <==

[2016-08-05T14:25:26.955] Launching batch job 7 for UID 1450

==> /home/galaxy/logs/handler0.log <==

galaxy.jobs.runners.drmaa DEBUG 2016-08-05 14:25:27,244 (2438/7) state change: job is running

==> /var/log/nginx/access.log <==

172.17.0.1 - admin [05/Aug/2016:14:25:30 +0000] "GET /api/histories/b701da857886499b/contents?v=dev&q=update_time-ge&qv=2016-08-05T14%3A25%3A26.000Z HTTP/1.1" 200 33 "http://129.69.102.30:8080/root <http://129.69.102.30:8080/root> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

==> /home/galaxy/logs/slurmctld.log <==

[2016-08-05T14:25:30.946] completing job 7

[2016-08-05T14:25:30.947] sched: job_complete for JobId=7 successful, exit code=0

==> /home/galaxy/logs/slurmd.log <==

[2016-08-05T14:25:30.945] [7] sending REQUEST_COMPLETE_BATCH_SCRIPT, error:0

[2016-08-05T14:25:30.947] [7] done with job

I will check if anything is wrong on that side...

-----Original message-----
From: Peter Cock <p.j.a.cock@googlemail.com>
Sent: Friday 5th August 2016 16:15
To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>
Cc: galaxy-dev@lists.galaxyproject.org; Brad Chapman <chapmanb@50mail.com>
Subject: Re: [galaxy-dev] conversion issue

I think you will need to look at the Galaxy logs for some clues
about if the dependencies are being found or not. The simple
"hack" is to install them on the $PATH manually, which would
be the practical solution if this is urgent.

Peter

On Fri, Aug 5, 2016 at 3:09 PM, Rathert, Philipp, Dr.
<philipp.rathert@ibc.uni-stuttgart.de> wrote:
...
Yes I did.
All tools are installed and I see no error message.
Philipp
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