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.c...@googlemail.com>
Sent: Friday 5th August 2016 16:15
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>
Cc: galaxy-dev@lists.galaxyproject.org; Brad Chapman <chapm...@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.rath...@ibc.uni-stuttgart.de> wrote:
> Yes I did.
> All tools are installed and I see no error message.
>
> Philipp

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