Dear All,
I get the following errors when I try to Convert BAM to BigWig
Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 103, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 48, in main convert_to_graph(bam_file, split, config, temp_handle) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 76, in convert_to_graph subprocess.check_call(cl, stdout=out_handle) File "/usr/lib/python2.7/subprocess.py", line 535, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() 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
The tool produced the following additional output:
Have 93 references Calculating coverage...
or
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/tmp2F67r6', '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned non-zero exit status 255
The tool produced the following additional output:
Have 93 references Calculating coverage... Converting 0 MB graph file to bigwig..
depending what version of the tool i am using.
Any idea what this can be?
I am using the latest Docker-galaxy-stable version (16.04) but I think this is not related to docker. All tools are updated.
Thank you very much for your help,
Philipp
Its sounds like bedGraphToBigWig has not been installed.
https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/
The README says:
Ensure the following command line tools are on the system path:
pysam - Python interface to samtools (http://code.google.com/p/pysam/) genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/) bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
However, the tool does appear to declare the dependencies via the Tool Shed mechanism - did you install them via the Tool Shed?
Peter
On Fri, Aug 5, 2016 at 2:23 PM, Rathert, Philipp, Dr. philipp.rathert@ibc.uni-stuttgart.de wrote:
Dear All,
I get the following errors when I try to Convert BAM to BigWig
Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 103, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 48, in main convert_to_graph(bam_file, split, config, temp_handle) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py", line 76, in convert_to_graph subprocess.check_call(cl, stdout=out_handle) File "/usr/lib/python2.7/subprocess.py", line 535, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() 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
The tool produced the following additional output:
Have 93 references Calculating coverage...
or
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/tmp2F67r6', '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned non-zero exit status 255
The tool produced the following additional output:
Have 93 references Calculating coverage... Converting 0 MB graph file to bigwig..
depending what version of the tool i am using.
Any idea what this can be?
I am using the latest Docker-galaxy-stable version (16.04) but I think this is not related to docker. All tools are updated.
Thank you very much for your help,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Yes I did. All tools are installed and I see no error message.
Philipp
---Philipp on the road---
Am 05.08.2016 um 15:31 schrieb Peter Cock <p.j.a.cock@googlemail.com mailto:p.j.a.cock@googlemail.com >:
Its sounds like bedGraphToBigWig has not been installed.
https://toolshed.g2.bx.psu.edu/view/brad-chapman/bam_to_bigwig/
The README says:
Ensure the following command line tools are on the system path:
pysam - Python interface to samtools (http://code.google.com/p/pysam/ http://code.google.com/p/pysam/ ) genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/ http://code.google.com/p/bedtools/ ) bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/ http://hgdownload.cse.ucsc.edu/admin/exe/ )
However, the tool does appear to declare the dependencies via the Tool Shed mechanism - did you install them via the Tool Shed?
Peter
On Fri, Aug 5, 2016 at 2:23 PM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de mailto:philipp.rathert@ibc.uni-stuttgart.de > wrote:
Dear All,
I get the following errors when I try to Convert BAM to BigWig
Traceback (most recent call last): File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py http://toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py ", line 103, in <module> main(*args, **kwargs) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py http://toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py ", line 48, in main convert_to_graph(bam_file, split, config, temp_handle) File "/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py http://toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/52bcd04ee0d6/bam_to_bigwig/bam_to_bigwig/bam_to_bigwig.py ", line 76, in convert_to_graph subprocess.check_call(cl, stdout=out_handle) File "/usr/lib/python2.7/subprocess.py", line 535, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() 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
The tool produced the following additional output:
Have 93 references Calculating coverage...
or
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 http://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 http://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 http://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/tmp2F67r6', '/export/galaxy-central/database/files/003/dataset_3116-sizes.txt', '/export/galaxy-central/database/files/003/dataset_3116.dat']' returned non-zero exit status 255
The tool produced the following additional output:
Have 93 references Calculating coverage... Converting 0 MB graph file to bigwig..
depending what version of the tool i am using.
Any idea what this can be?
I am using the latest Docker-galaxy-stable version (16.04) but I think this is not related to docker. All tools are updated.
Thank you very much for your help,
Philipp
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ http://galaxyproject.org/search/mailinglists/
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
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
galaxy-dev@lists.galaxyproject.org
-
Peter Cock -
Rathert, Philipp, Dr.