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Configuring Galaxy, Pulsar and Conda

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Configuring Galaxy, Pulsar and Conda

ric
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: [hidden email]
Website: www.crs4.it
 

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Re: Configuring Galaxy, Pulsar and Conda

John Chilton-4
Hello,

Thanks for working on this - Pulsar still hasn't quite caught up with
Galaxy in terms of support for Conda but we are getting there. So I
noticed two things that should help today when I was trying to
recreate your problem - the first is that Conda support in Pulsar
requires this PR (https://github.com/galaxyproject/pulsar/pull/126)
which isn't part of 0.7.3 - the pulsar you are targeting. I did an
update of Pulsar though so that should help - release 0.7.4 should be
available as of today.

Additionally, I noticed that the default for the Pulsar client option
"dependency_resolution" in Galaxy was broken. So to get this to work
at all - you will need to update your job_conf.xml and specify that
Pulsar should resolve dependencies and not Galaxy. This means adding
<param id="dependency_resolution">remote</param> to your Pulsar
destination. I opened a Pull Request here for the Galaxy change - so
hopefully this will be the default by the time 17.01 is released.

The logs should make it clear if there are additional problems after
those changes I think. One think I would recommend is adding a
versionless Conda resolver also - so you may want to make that
dependency resolvers file look like this instead:

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

This may not be strictly needed based on the tools you are attempting
to get this to work for though.

Thanks for your patience and let me know how it goes.

-John



On Fri, Feb 3, 2017 at 6:18 AM, ric <[hidden email]> wrote:

> 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: [hidden email]
> Website: www.crs4.it
>
> ___________________________________________________________
> 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/
>
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>  http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
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Re: Configuring Galaxy, Pulsar and Conda

ric
Hi John, thank you for your help.
Now it works!



Il 07/02/2017 21:20, John Chilton ha scritto:

> Hello,
>
> Thanks for working on this - Pulsar still hasn't quite caught up with
> Galaxy in terms of support for Conda but we are getting there. So I
> noticed two things that should help today when I was trying to
> recreate your problem - the first is that Conda support in Pulsar
> requires this PR (https://github.com/galaxyproject/pulsar/pull/126)
> which isn't part of 0.7.3 - the pulsar you are targeting. I did an
> update of Pulsar though so that should help - release 0.7.4 should be
> available as of today.
>
> Additionally, I noticed that the default for the Pulsar client option
> "dependency_resolution" in Galaxy was broken. So to get this to work
> at all - you will need to update your job_conf.xml and specify that
> Pulsar should resolve dependencies and not Galaxy. This means adding
> <param id="dependency_resolution">remote</param> to your Pulsar
> destination. I opened a Pull Request here for the Galaxy change - so
> hopefully this will be the default by the time 17.01 is released.
>
> The logs should make it clear if there are additional problems after
> those changes I think. One think I would recommend is adding a
> versionless Conda resolver also - so you may want to make that
> dependency resolvers file look like this instead:
>
> <dependency_resolvers>
>      <conda auto_install="True" auto_init="True" />
>      <conda auto_install="True" auto_init="True" versionless="True" />
> </dependency_resolvers>
>
> This may not be strictly needed based on the tools you are attempting
> to get this to work for though.
>
> Thanks for your patience and let me know how it goes.
>
> -John
>
>
>
> On Fri, Feb 3, 2017 at 6:18 AM, ric <[hidden email]> wrote:
>> 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: [hidden email]
>> Website: www.crs4.it
>>
>> ___________________________________________________________
>> 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/


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

___________________________________________________________
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