Re: [galaxy-dev] Problem installing local instance of Galaxy
Hi Kenneth If you try to connect to localhost using your PC, it will search for a (galaxy)server on your PC. Hence, you need to replace localhost with the name or IP adress of the server where Galaxy is running Regards, Hans On 08/17/2012 03:24 AM, Kenneth Watanabe wrote: To Galaxy, I installed Galaxy on my local server.. I modified the universe_wsgi.ini file as follows: # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. host = 0.0.0.0 I type the following command at the LINUX prompt to start the service $ sh run.sh ... Starting server in PID 2685 serving on 0.0.0.0:8080 view at http://127.0.0.1:800 When I open FIrefox directly on the server and go to the web address http://localhost:8080 the galaxy screen appears. When I open FIrefox on my PC and go to http://localhost:8080, I get the following error Unable to connect Firefox can't establish a connection to the server at localhost:8080. Any suggestions would be greatly appreciated. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] FTP upload - symlink to uploaded data
Hi Nate, thanks. Do you know what's the reason for using copying first the contents to the /tmp directory, before copying it into a the database/files/... Seems inefficient to do so, or is this not how it works perhaps? Regards, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 08/16/2012 05:19 PM, Nate Coraor wrote: On Aug 16, 2012, at 11:09 AM, Joachim Jacob wrote: Excuses for the repost, but I really need to solve this. Uploading with FTP fails on our Galaxy, because the /tmp directory has not enough space. How can I hack in the Galaxy code base that the temporary directory needs to be /mnt/galaxydb/tmp ? Another solution: how can I provide a symlink to our FTP directory? Hi Joachim, It's not possible with the FTP upload method, but if you set user_library_import_dir in the config file, users can upload files from a server directory and choose the link option, just like an admin can. --nate Thanks for any hint, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 08/08/2012 12:12 PM, Joachim Jacob wrote: Dear devs, Question about FTP upload: is it correct that Galaxy copies the data from the FTP upload directory to galaxy database instead of symlinking? Can I set somewhere the option to symlink instead of copying? I run galaxy in a small virtual machine. The Galaxy database is on a network share. With 'get data' - 'Upload file', when importing the files I have uploaded with FTP, there is a process filling up the /tmp directory with the file I want to import. Kind regards, Joachim ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] optional=false not working?
On Fri, Aug 17, 2012 at 12:18 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hello, I have the following wrapper: tool id=foo name=foo version=0.99.0 descriptionfoo/description command interpreter=python tool.py $outputFileName /command inputs param name=tp type=text label=label help=help optional=false/ /inputs outputs data format=csv name=outputFileName/ /outputs /tool I expect that when I click Execute I will be told that tp must have a value. However, that doesn't happen, it just goes ahead and executes the script. How do I get Galaxy to require that a text param have a value? Thanks, Dan Probably is has the value of an empty string? That seems logical but unhelpful - and explains the behaviour ;) You can probably use a validator in the XML for this (e.g. insist on at least one character). Peter ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] cuffdiff output
Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). Output with reference annotation produced output with gene ids naming usc## Output without reference annotation produced output with gene ids naming CUFF1.### Can anyone suggest how to get gene names instead of just numbers? Thanks suz ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Track jobs in database should be True? Re: Shell script to start Galaxy in multi-server environment
On 8/16/12 4:18 PM, Karger, Amir amir_kar...@hms.harvard.edu wrote: On 8/8/12 4:06 PM, Nate Coraor n...@bx.psu.edu wrote: If you aren't setting job_manager and job_handlers in your config, each server will consider itself the manager and handler. If not configured to run jobs, this may result in jobs failing to run. I'd suggest explicitly defining a manager and handlers. --nate Sigh. We have both job_manager and job_handlers set to the same server. It seems like our runner app may be getting into some kind of sleeping state. I was unable to upload a file, which had worked before. However, when I restarted the runner, it picked up the upload job and successfully uploaded it AND picked up the previously queued tab2fasta job, and I believe completed it successfully too. Replying to myself. The reason the runner was in a sleep state is the logic in lib/galaxy/web/config.py says: if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] == self.server_name ) and ( self.job_manager == self.server_name ): self.track_jobs_in_database = False For our dev instance, we have a single server acting as the job manager and the job handler, and we have two web servers also running on the dev box. So Galaxy apparently decides not to track the jobs in the database. However, this means it never finds any jobs to run. When we explicitly set self.track_jobs_in_database to be true in config.py, Galaxy correctly finds and runs jobs. I guess the webapps think that Galaxy *is* tracking jobs in the database, so they put jobs in there that never get pulled out? Or should it actually work when track_jobs_in_database is false, as long as the job manager and job handler(and webapps?) are on the same server. In that case, do we know why it didn't work? I'm happy to be running track_jobs_in_database=True, because our prod server is going to have separate machines doing web vs. job handling/managing. Thanks, -Amir ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] grouping/separating parameters on the page
Hello, Is there a way to do one or both of the following: 1) Group a set of related parameters together on a tool page 2) Put a separator in between related groups. I have a tool with lots of parameters. It's ok to have them all on one page but I'd like to have some space or a line between the related groups (and maybe even a header for the group) so that users know which parameters are related. Thanks, Dan ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] code example for improved error handling
I'm writing documentation now - I'll have something this afternoon.
Sorry for the delay.
-Scott
- Original Message -
No, I call the executable directly from the xml. It kept failing
although it seemed to finish the job and I realized that on success
the executable prints a summary message to stderror, because it's
using stdout for the actual results so they can be pipped to another
command.
From the July news brief I understood that you can now add code to
the xml to check the stdout and std error for messages and I was
wondering if you have any documentation or sample code for that in
any published tool.
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
Genomics, Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.com
From: John Patterson jmpa...@g.uky.edu
Date: Thursday, August 16, 2012 12:29 PM
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] code example for improved error handling
On 08/16/2012 03:02 PM, Birgit Crain wrote:
Hi
I'm writing a tools for an executable that writes results to stdout
and reports success message to stderr, so it really need the
improved error handling. Is there any sample code or documentation
available?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist |
Complete
Genomics, Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.com
From: Nicole Rockweiler n.rockwei...@gmail.com
Date: Friday, July 20, 2012 10:53 AM
To: Brian Haas bh...@broadinstitute.org
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy
shows failure
Hi Brian,
A couple of days ago, smcmanus pushed the following change to the
repo:
Tools can now specify their own handling of stderr and stdout
regular
expressions as well as exit code ranges.
https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-job
It looks like the documentation has yet to be written.
Hope this helps,
Nicole
On Fri, Jul 20, 2012 at 12:46 PM, Brad Chapman
chapm...@50mail.com
wrote:
Brian;
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the
output
file accessible as a new data set.
Is it possible the software is writing to standard error? Galaxy
doesn't
check status codes, but rather check for stderr and assumes that
output
indicates a problem. You can wrap the problematic programs with a
little
script to eat up stderr and check that everything is okay:
http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
Brad
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's captured
the
output, but in the display of the web browser, it just shows up
in
the
error state. The script being run exits (0) on success. Any
ideas?
Here's what the output section of my xml file looks like:
outputs
data format=bam name=coordSortedBam label=${ tool.name }
on ${on_string}: coord-sorted read alignments
from_work_dir=alignment/alignment.coordSorted.bam/
/outputs
and here's what the server log states:
galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job
dispatched
galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453
executing:
alignReads.pl --target
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat
-o alignment --aligner bowtie --single
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat
--seqType fq
galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam
to
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat
as directed by from_work_dir
Again, as far as I can tell, everything worked - but the
browser
doesn't think so.
I've run the exact command above on the command-line, and it
exits(0)
indicating success.
Also, I've verified that when run through my galaxy instance,
the
galaxy-relocated output file is as expected.
Many thanks for your help. I'm still getting my feet wet with
galaxy, reading through all the documentation and searching the
mailing list for additional help.
best regards,
-brian
Re: [galaxy-dev] code example for improved error handling
Thanks, greatly appreciated!
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics,
Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.commailto:bcr...@completegenomics.com
From: Scott McManus scottmcma...@gatech.edumailto:scottmcma...@gatech.edu
Date: Friday, August 17, 2012 11:02 AM
To: Birgit Crain
bcr...@completegenomics.commailto:bcr...@completegenomics.com
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] code example for improved error handling
I'm writing documentation now - I'll have something this afternoon.
Sorry for the delay.
-Scott
No, I call the executable directly from the xml. It kept failing although it
seemed to finish the job and I realized that on success the executable prints a
summary message to stderror, because it's using stdout for the actual results
so they can be pipped to another command.
From the July news brief I understood that you can now add code to the xml to
check the stdout and std error for messages and I was wondering if you have
any documentation or sample code for that in any published tool.
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics,
Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.commailto:bcr...@completegenomics.com
From: John Patterson jmpa...@g.uky.edumailto:jmpa...@g.uky.edu
Date: Thursday, August 16, 2012 12:29 PM
To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] code example for improved error handling
On 08/16/2012 03:02 PM, Birgit Crain wrote:
Hi
I'm writing a tools for an executable that writes results to stdout and reports
success message to stderr, so it really need the improved error handling. Is
there any sample code or documentation available?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics,
Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.commailto:bcr...@completegenomics.com
From: Nicole Rockweiler n.rockwei...@gmail.commailto:n.rockwei...@gmail.com
Date: Friday, July 20, 2012 10:53 AM
To: Brian Haas bh...@broadinstitute.orgmailto:bh...@broadinstitute.org
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy shows failure
Hi Brian,
A couple of days ago, smcmanushttps://bitbucket.org/smcmanus pushed the
following change to the repo:
Tools can now specify their own handling of stderr and stdout regular
expressions as well as exit code ranges.
https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-job
It looks like the documentation has yet to be written.
Hope this helps,
Nicole
On Fri, Jul 20, 2012 at 12:46 PM, Brad Chapman
chapm...@50mail.commailto:chapm...@50mail.com wrote:
Brian;
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the output
file accessible as a new data set.
Is it possible the software is writing to standard error? Galaxy doesn't
check status codes, but rather check for stderr and assumes that output
indicates a problem. You can wrap the problematic programs with a little
script to eat up stderr and check that everything is okay:
http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
Brad
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's captured the
output, but in the display of the web browser, it just shows up in the
error state. The script being run exits (0) on success. Any ideas?
Here's what the output section of my xml file looks like:
outputs
data format=bam name=coordSortedBam
label=${tool.namehttp://tool.name}
on ${on_string}: coord-sorted read alignments
from_work_dir=alignment/alignment.coordSorted.bam/
/outputs
and here's what the server log states:
galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job dispatched
galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453 executing:
alignReads.pl --target
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat
-o alignment --aligner bowtie --single
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat
--seqType fq
galaxy.jobshttp://galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam
to /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat
as directed by from_work_dir
Again, as far as I can tell, everything worked - but the browser
doesn't think so.
[galaxy-dev] TopHat Wrapper to handle Multiple Fastq reads
Greetings, I was working on the TopHat wrapper (we have customized one for handling just one input Fastq read) for handling multiple reads. I figured out that using repeat tag was the way forward, but have been having a hard time with the Cheetah template. Any help or suggestions? Sincerely, Vijay ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy Reports no longer functions
Hi Team, Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_webapp.log is as follows: python path is: /hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 'recursive' middleware /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 'x-forwarded-host' middleware Starting server in PID 6345. Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 303, in command serve() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 287, in serve server(app) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 151, in server_wrapper **context.local_conf) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) File /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1314, in server_runner
Re: [galaxy-dev] code example for improved error handling
Please see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax .
There is a section for stdio, regex, and exit_code tag sets. The
documentation
applies to the latest galaxy-dist, though most of what's mentioned (aside from
updating
stdout and stderr with warning messages) is supported in galaxy-central.
(You can also use the fairly ugly URL
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets
).
-Scott
- Original Message -
Hi
I'm writing a tools for an executable that writes results to stdout
and reports success message to stderr, so it really need the
improved error handling. Is there any sample code or documentation
available?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
Genomics, Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.com
From: Nicole Rockweiler n.rockwei...@gmail.com
Date: Friday, July 20, 2012 10:53 AM
To: Brian Haas bh...@broadinstitute.org
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy
shows failure
Hi Brian,
A couple of days ago, smcmanus pushed the following change to the
repo:
Tools can now specify their own handling of stderr and stdout
regular
expressions as well as exit code ranges.
https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-job
It looks like the documentation has yet to be written.
Hope this helps,
Nicole
On Fri, Jul 20, 2012 at 12:46 PM, Brad Chapman chapm...@50mail.com
wrote:
Brian;
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the
output
file accessible as a new data set.
Is it possible the software is writing to standard error? Galaxy
doesn't
check status codes, but rather check for stderr and assumes that
output
indicates a problem. You can wrap the problematic programs with a
little
script to eat up stderr and check that everything is okay:
http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
Brad
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's captured
the
output, but in the display of the web browser, it just shows up
in
the
error state. The script being run exits (0) on success. Any
ideas?
Here's what the output section of my xml file looks like:
outputs
data format=bam name=coordSortedBam label=${ tool.name }
on ${on_string}: coord-sorted read alignments
from_work_dir=alignment/alignment.coordSorted.bam/
/outputs
and here's what the server log states:
galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job
dispatched
galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453
executing:
alignReads.pl --target
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat
-o alignment --aligner bowtie --single
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat
--seqType fq
galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam
to
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat
as directed by from_work_dir
Again, as far as I can tell, everything worked - but the browser
doesn't think so.
I've run the exact command above on the command-line, and it
exits(0)
indicating success.
Also, I've verified that when run through my galaxy instance, the
galaxy-relocated output file is as expected.
Many thanks for your help. I'm still getting my feet wet with
galaxy, reading through all the documentation and searching the
mailing list for additional help.
best regards,
-brian
--
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
tool id=alignreads name=alignReads version=0.0.1
descriptionalignReads: short read alignment tool
wrapper/description
requirements
requirement type=packagetrinity/requirement
/requirements
command
alignReads.pl --target $target -o alignment --aligner
$aligner_selection.aligner
## Inputs.
#if str($inputs.paired_or_single) == paired:
--left $inputs.left_input --right $inputs.right_input
#if $inputs.left_input.ext == 'fa':
--seqType fa
#else:
--seqType fq
#end if
#if str($inputs.library_type) != None:
--SS_lib_type $inputs.library_type
#end if
