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
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
[galaxy-dev] code example for improved error handling
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.
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
--max_dist_between_pairs $inputs.max_dist_between_pairs
#else:
--single $inputs.input
#if str($inputs.input.ext) == 'fa':
--seqType fa
#else:
--seqType fq
#end if
#if str($inputs.library_type) != None:
--SS_lib_type $inputs.library_type
#end if
#end if
## Additional parameters.
##if str($inputs.use_additional) == yes:
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 mailto:bcr...@completegenomics.com
From: Nicole Rockweiler n.rockwei...@gmail.com
mailto:n.rockwei...@gmail.com
Date: Friday, July 20, 2012 10:53 AM
To: Brian Haas bh...@broadinstitute.org
mailto:bh...@broadinstitute.org
Cc: galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu
galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy shows
failure
Hi Brian,
A couple of days ago, smcmanus https://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.com
mailto: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 http://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 http://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 http://broad.mit.edu/%7Ebhaas
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
Re: [galaxy-dev] code example for improved error handling
On Thu, Aug 16, 2012 at 8:02 PM, Birgit Crain bcr...@completegenomics.com 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 No documentation yet that I know of - I'm waiting too, but the code to support this has been committed, see: https://bitbucket.org/galaxy/galaxy-central/issue/325/ 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/
Re: [galaxy-dev] code example for improved error handling
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.
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/~bhaashttp://broad.mit.edu/%7Ebhaas
tool id=alignreads name=alignReads version=0.0.1
descriptionalignReads: short read alignment tool wrapper/description
requirements
requirement type=packagetrinity
