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
remote 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:
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
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=hid=dev=update_time-ge=deleted=purged=2017-01-19T12%3A11%3A40.000Z=False=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 , None: metaclass conflict: the
metaclass of a derived class must be a (non-stri
