[galaxy-dev] Configuring Galaxy, Pulsar and Conda

Fri, 03 Feb 2017 03:18:59 -0800 

Hi,
I'm tryng to configure a Pulsar server to resolve dependencies using Conda but unfortunately it does not work. When I try to execute, for example, bowtie2, the standard error in the Galaxy machine says: "/home/galaxy/pulsar/files/staging/67/command.sh: line 60: bowtie2-build: command not found" because Conda in the Pulsar machine does not download this dependency. 

Here is my app.yml:

dependency_resolvers_config_file: dependency_resolvers_conf.xml


My dependency_resolvers_conf.xml

<dependency_resolvers>
    <conda auto_install="True" auto_init="True" />
</dependency_resolvers>


The log of the Galaxy server:


galaxy.tools DEBUG 2017-01-19 14:50:18,910 Validated and populated state 
for tool request (97.265 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,069 Handled output named 
output for tool 
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0 (81.926 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,113 Added output datasets 
to history (43.950 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,179 Verified access to 
datasets for 
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] 
(33.690 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,180 Setup for job 
Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] 
complete, ready to flush (66.261 ms)
galaxy.tools.actions INFO 2017-01-19 14:50:19,240 Flushed transaction 
for job 
Job[id=67,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] 
(59.840 ms)
galaxy.tools.execute DEBUG 2017-01-19 14:50:19,240 Tool 
[toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] created job 
[67] (296.972 ms)
galaxy.tools.execute DEBUG 2017-01-19 14:50:19,266 Executed 1 job(s) for 
tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0 request: 
(355.402 ms)
156.148.160.117 - - [19/Jan/2017:14:50:18 +0200] "POST /api/tools 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:19 +0200] "GET /api/webhooks/tool 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:19 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T12%3A11%3A40.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
galaxy.jobs DEBUG 2017-01-19 14:50:19,912 (67) Working directory for job 
is: /home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67
galaxy.jobs.handler DEBUG 2017-01-19 14:50:19,931 (67) Dispatching to 
pulsar runner
galaxy.jobs DEBUG 2017-01-19 14:50:20,013 (67) Persisting job 
destination (destination id: remote_cluster)
galaxy.jobs.runners DEBUG 2017-01-19 14:50:20,044 Job [67] queued 
(112.446 ms)

galaxy.jobs.handler INFO 2017-01-19 14:50:20,090 (67) Job dispatched

galaxy.jobs.runners.pulsar INFO 2017-01-19 14:50:20,205 pulsar_version 
is 0.7.3
galaxy.util.object_wrapper WARNING 2017-01-19 14:50:20,644 Unable to 
create dynamic subclass for <type 'instance'>, None: metaclass conflict: 
the metaclass of a derived class must be a (non-strict) subclass of the 
metaclasses of all its bases
galaxy.tools.deps DEBUG 2017-01-19 14:50:20,820 Find dependency bowtie2 
version 2.3.0
galaxy.tools.deps DEBUG 2017-01-19 14:50:20,821 Using dependency bowtie2 
version 2.3.0 of type conda
galaxy.tools.deps DEBUG 2017-01-19 14:50:20,821 Find dependency samtools 
version 1.3.1
galaxy.tools.deps DEBUG 2017-01-19 14:50:20,821 Using dependency 
samtools version 1.3.1 of type conda
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:20,822 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
list --name __bowtie2@2.3.0 --export > 
./database/tmp/jobdepsUaJpU60c3b56cd60a211bacfadd5c45280e5adba95113fa75f9e47b09cad555f49ae2b/__bowtie2@2.3.0
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:21,220 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
create -y --unknown --offline --prefix 
/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/conda-env 
--copy --file 
./database/tmp/jobdepsUaJpU60c3b56cd60a211bacfadd5c45280e5adba95113fa75f9e47b09cad555f49ae2b/__bowtie2@2.3.0 
> /dev/null
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:23,885 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
clean --tarballs -y
156.148.160.117 - - [19/Jan/2017:14:50:24 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A19.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"

Cache location:
There are no tarballs to remove

galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:24,291 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
list --name __samtools@1.3.1 --export > 
./database/tmp/jobdepsGUOeaPf795a38a38496af1ff491d0cf89e7e5d9fe737e5c36da3dd56c71ad608bb9b15/__samtools@1.3.1
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:24,672 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
install -y --unknown --offline --prefix 
/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/conda-env 
--copy --file 
./database/tmp/jobdepsGUOeaPf795a38a38496af1ff491d0cf89e7e5d9fe737e5c36da3dd56c71ad608bb9b15/__samtools@1.3.1 
> /dev/null
156.148.160.117 - - [19/Jan/2017:14:50:24 +0200] "POST 
/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0/build 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:25,251 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
clean --tarballs -y

Cache location:
There are no tarballs to remove

pulsar.client.client DEBUG 2017-01-19 14:50:25,904 Uplodaing path 
[/home/galaxy/galaxy_test_pulsar/database/files/000/dataset_65.dat] 
(action_type: [transfer])
pulsar.client.client DEBUG 2017-01-19 14:50:25,913 Uplodaing path 
[/home/galaxy/galaxy_test_pulsar/database/files/000/dataset_59.dat] 
(action_type: [transfer])
156.148.160.117 - - [19/Jan/2017:14:50:28 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A24.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:32 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A28.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:37 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A32.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:41 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A37.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:45 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A41.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:50:50 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A45.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
galaxy.jobs.runners.pulsar INFO 2017-01-19 14:50:55,332 Pulsar job 
submitted with job_id 67
galaxy.jobs DEBUG 2017-01-19 14:50:55,333 (67) Persisting job 
destination (destination id: remote_cluster)
156.148.160.117 - - [19/Jan/2017:14:50:55 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A50.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
pulsar.client.staging.down INFO 2017-01-19 14:50:57,558 collecting 
output COMMAND_VERSION with action FileAction[action_type=transfer]
pulsar.client.staging.down DEBUG 2017-01-19 14:50:57,562 Cleaning up job 
(failed [False], cleanup_job [always])
galaxy.tools.deps DEBUG 2017-01-19 14:50:59,176 Find dependency samtools 
version None
galaxy.tools.deps DEBUG 2017-01-19 14:50:59,176 Using dependency 
samtools version None of type conda
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:59,177 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
list --name __samtools@_uv_ --export > 
./database/tmp/jobdepsgV6rJH373e7bbee36e032187809f77033895b78158b1575365caf0cada674b44d010b8/__samtools@_uv_
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:59,558 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
install -y --unknown --offline --prefix 
/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/conda-env 
--copy --file 
./database/tmp/jobdepsgV6rJH373e7bbee36e032187809f77033895b78158b1575365caf0cada674b44d010b8/__samtools@_uv_ 
> /dev/null
156.148.160.117 - - [19/Jan/2017:14:50:59 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A55.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
galaxy.tools.deps.conda_util DEBUG 2017-01-19 14:50:59,967 Executing 
command: 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/conda 
clean --tarballs -y

Cache location:
There are no tarballs to remove

galaxy.jobs.runners DEBUG 2017-01-19 14:51:00,351 executing external 
set_meta script for job 67: [ "$CONDA_DEFAULT_ENV" = 
"/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/conda-env" 
] || . 
/home/galaxy/galaxy_test_pulsar/database/dependencies/_conda/bin/activate '/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/conda-env' 
> conda_activate.log 2>&1 
&&GALAXY_LIB="/home/galaxy/galaxy_test_pulsar/lib"; if [ "$GALAXY_LIB" 
!= "None" ]; then if [ -n "$PYTHONPATH" ]; then 
PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; 
export PYTHONPATH; fi; 
GALAXY_VIRTUAL_ENV="/home/galaxy/galaxy_test_pulsar/.venv"; if [ 
"$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f 
"$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . 
"$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python 
"/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/set_metadata_6JXZtD.py" 
"/home/galaxy/galaxy_test_pulsar/database/tmp/tmpqS9WNY" 
"/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/working/galaxy.json" 
"/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/metadata_in_HistoryDatasetAssociation_71_TIRfAD,/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/metadata_kwds_HistoryDatasetAssociation_71_drHgz4,/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/metadata_out_HistoryDatasetAssociation_71_AQg1tP,/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/metadata_results_HistoryDatasetAssociation_71_E1N138,/home/galaxy/galaxy_test_pulsar/database/files/000/dataset_71.dat,/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/metadata_override_HistoryDatasetAssociation_71_iGnttD" 
5242880

Traceback (most recent call last):

  File 
"/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/set_metadata_6JXZtD.py", 
line 1, in <module>
    from galaxy_ext.metadata.set_metadata import set_metadata; 
set_metadata()

ImportError: No module named galaxy_ext.metadata.set_metadata

galaxy.jobs.runners DEBUG 2017-01-19 14:51:01,013 execution of external 
set_meta for job 67 finished

galaxy.jobs INFO 2017-01-19 14:51:03,230 Collecting metrics for Job 67

galaxy.jobs DEBUG 2017-01-19 14:51:03,261 job 67 ended (finish() 
executed in (2246.565 ms))
galaxy.model.metadata DEBUG 2017-01-19 14:51:03,272 Cleaning up external 
metadata files
galaxy.model.metadata DEBUG 2017-01-19 14:51:03,317 Failed to cleanup 
MetadataTempFile temp files from 
/home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67/metadata_out_HistoryDatasetAssociation_71_AQg1tP: 
No JSON object could be decoded
156.148.160.117 - - [19/Jan/2017:14:51:04 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T13%3A50%3A59.000Z&qv=False&qv=False 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:04 +0200] "GET 
/api/histories/1cd8e2f6b131e891?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:04 +0200] "POST 
/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0/build 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:07 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents/datasets/fa6833a4eadf9064 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:16 +0200] "GET 
/datasets/fa6833a4eadf9064/show_params HTTP/1.1" 200 - 
"http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:22 +0200] "GET 
/datasets/fa6833a4eadf9064/stderr HTTP/1.1" 200 - 
"http://156.148.120.96:8080/datasets/fa6833a4eadf9064/show_params"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/55.0.2883.87 Safari/537.36"
/home/galaxy/galaxy_test_pulsar/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: 
SAWarning: The IN-predicate on "request_type.id" was invoked with an 
empty sequence. This results in a contradiction, which nonetheless can 
be expensive to evaluate.  Consider alternative strategies for improved 
performance.

  'strategies for improved performance.' % expr)

156.148.160.117 - - [19/Jan/2017:14:51:45 +0200] "GET /admin HTTP/1.1" 
200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:45 +0200] "GET 
/admin/center?status=done&message= HTTP/1.1" 200 - 
"http://156.148.120.96:8080/admin"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:47 +0200] "GET 
/api/webhooks/masthead/all HTTP/1.1" 200 - 
"http://156.148.120.96:8080/admin"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:50 +0200] "GET 
/admin_toolshed/browse_tool_sheds HTTP/1.1" 200 - 
"http://156.148.120.96:8080/admin"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:51:52 +0200] "GET 
/admin_toolshed/browse_tool_shed?tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F 
HTTP/1.1" 302 - 
"http://156.148.120.96:8080/admin_toolshed/browse_tool_sheds"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/55.0.2883.87 Safari/537.36"
galaxy.managers.users WARNING 2017-01-19 14:59:17,048 
{u'RepositoryInstallationGrid.filter': u'{}', 
u'RepositoryInstallationGrid.sort_key': u'"-create_time"'}
156.148.160.117 - - [19/Jan/2017:14:59:16 +0200] "GET / HTTP/1.1" 200 - 
"http://156.148.120.96:8080/admin"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:19 +0200] "GET 
/api/webhooks/history-menu/all HTTP/1.1" 200 - 
"http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:19 +0200] "GET 
/api/datatypes?extension_only=False HTTP/1.1" 200 - 
"http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:19 +0200] "GET 
/api/webhooks/masthead/all HTTP/1.1" 200 - "http://156.148.120.96:8080/"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:19 +0200] "GET /api/genomes 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:19 +0200] "GET /welcome HTTP/1.1" 
302 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:19 +0200] "GET 
/history/current_history_json HTTP/1.1" 200 - 
"http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
galaxy.managers.users WARNING 2017-01-19 14:59:20,083 
{u'RepositoryInstallationGrid.filter': u'{}', 
u'RepositoryInstallationGrid.sort_key': u'"-create_time"'}
156.148.160.117 - - [19/Jan/2017:14:59:20 +0200] "GET 
/api/users/f597429621d6eb2b HTTP/1.1" 200 - 
"http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:20 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?limit=500&offset=0&details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b%2Cfa6833a4eadf9064&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:21 +0200] "GET 
/api/histories/1cd8e2f6b131e891?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:23 +0200] "GET 
/api/histories/1cd8e2f6b131e891/contents?keys=type_id%2Celement_count&details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b%2Cfa6833a4eadf9064&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True 
HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux 
x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 
Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:24 +0200] "GET 
/datasets/fa6833a4eadf9064/show_params HTTP/1.1" 200 - 
"http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36"
156.148.160.117 - - [19/Jan/2017:14:59:27 +0200] "GET 
/datasets/fa6833a4eadf9064/stderr HTTP/1.1" 200 - 
"http://156.148.120.96:8080/datasets/fa6833a4eadf9064/show_params"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/55.0.2883.87 Safari/537.36"




The log of the Pulsar server:

Sourcing file ./local_env.sh
Starting pulsar with command [paster server "./server.ini" ""]

2017-01-19 14:49:36,769 INFO  [pulsar.core][MainThread] Starting the 
Pulsar without a toolbox to white-list.Ensure this application is 
protected by firewall or a configured private token.
2017-01-19 14:49:36,793 INFO  [pulsar.locks][MainThread] pylockfile 
module not found, skipping experimental lockfile handling.

Starting server in PID 12234.
serving on 0.0.0.0:8913 view at http://127.0.0.1:8913

2017-01-19 14:50:31,715 DEBUG [pulsar.web.routes][worker 0] Setup job 
with configuration: {'tool_id': 
u'toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0', 
'metadata_directory': '/home/galaxy/pulsar/files/staging/67/metadata', 
'tool_version': u'2.3.0', 'path_separator': '/', 
'unstructured_files_directory': 
'/home/galaxy/pulsar/files/staging/67/unstructured', 'tools_directory': 
'/home/galaxy/pulsar/files/staging/67/tool_files', 'working_directory': 
'/home/galaxy/pulsar/files/staging/67/working', 'inputs_directory': 
'/home/galaxy/pulsar/files/staging/67/inputs', 'job_directory': 
'/home/galaxy/pulsar/files/staging/67', 'system_properties': 
{'galaxy_home': '/home/galaxy/galaxy_test_pulsar', 'separator': '/'}, 
'outputs_directory': '/home/galaxy/pulsar/files/staging/67/outputs', 
'job_id': '67', 'configs_directory': 
'/home/galaxy/pulsar/files/staging/67/configs', 'pulsar_version': '0.7.3'}
2017-01-19 14:51:06,843 DEBUG 
[pulsar.managers.base][[manager=_default_]-[action=preprocess]-[job=67]] 
job_id: 67 - Checking authorization of command_line [bowtie2 --version > 
/home/galaxy/pulsar/files/staging/67/outputs/COMMAND_VERSION 2>&1; 
bowtie2-build --threads ${GALAXY_SLOTS:-4} 
'/home/galaxy/pulsar/files/staging/67/inputs/dataset_59.dat' genome && 
ln -s -f '/home/galaxy/pulsar/files/staging/67/inputs/dataset_59.dat' 
genome.fa &&   bowtie2  -p ${GALAXY_SLOTS:-4}  -x 'genome' -U 
'/home/galaxy/pulsar/files/staging/67/inputs/dataset_65.dat' | samtools 
sort -O bam -o 
'/home/galaxy/pulsar/files/staging/67/outputs/dataset_71.dat'; 
return_code=$?; sh -c "exit $return_code"]
2017-01-19 14:51:07,826 INFO 
[pulsar.client.staging.down][[manager=_default_]-[action=postprocess]-[job=67]] 
collecting output COMMAND_VERSION with action 
FileAction[action_type=transfer]
2017-01-19 14:51:07,827 INFO 
[pulsar.managers.stateful][[manager=_default_]-[action=postprocess]-[job=67]] 
Status of job [67] changed to [complete]. No callbacks enabled.





I think I'm doing something wrong in the configuration of the Pulsar 
server so I need some help or suggestion.



Thank you

--
Ricardo Medda
CRS4 - Biomedicina
Phone +39 070 9250 ???
Loc. Pixina Manna Edificio 1
Pula 09010 (CA), Italy
Email: me...@crs4.it
Website: www.crs4.it

 


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