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 <me...@crs4.it> 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: me...@crs4.it
> Website: www.crs4.it
>
> ___________________________________________________________
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