Re: [galaxy-dev] setting up the drmaa for sge
Hello, Can you run a job with qsub from your Galaxy server with your Galaxy user ? Thomas -- Thomas Bellembois, network and system administrator ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE +33 4 26 73 13 67 .The IGFL is a member of the portail-labos project (https://portail-labos.ens-lyon.fr/site/). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc On 21/01/2014 22:16, Cantarel, Brandi L. wrote: Hi all, I have been trying to set up my galaxy instance to use SGE -- I created a job_conf.xml using the sample as a model and updated the galaxy user bashrc with the DRMAA_LIBRARY_PATH export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so But when I try to add data to a library I get the error: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Not too comforting since I am the administrator. The error in the log says: galaxy.jobs.handler DEBUG 2014-01-21 14:57:39,478 (2) Dispatching to drmaa runner galaxy.jobs.handler ERROR 2014-01-21 14:57:39,479 put(): (2) Invalid job runner: drmaa What does that mean, Invalid job runner? Does this mean I have an error in my job_conf.xml? Here is my job_conf.xml ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=main tags=handlers/ /handlers destinations default=sge_default !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=sge_default runner=drmaa/ !-- Define parameters that are native to the job runner plugin. -- /destinations /job_conf Thanks for your help! ~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] http_proxy environment kills run_functional_tests.sh
Dear Gal-dev-ians, I just made a discovery and thought to share it with others so that they could save time and perhaps it gets documented in the maintained documentation. Namely, if http_proxy is set before running the run_functional_tests.sh, then all tests fails. This is due to the fact that twil tries to use the http_proxy for ALL connections, also those to the localhost. I just stumbled across it, while trying to fix the twill problems that I was getting without http_proxy... Wish you all a galactical day and hope with this mail to save time (to at least the newcomers). L. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting up the drmaa for sge
Are you asking if I can submit jobs to sge with the galaxy user on the server — yes, I can, at least I can on the command line... On Jan 22, 2014, at 3:00 AM, Thomas Bellembois thomas.bellemb...@ens-lyon.frmailto:thomas.bellemb...@ens-lyon.fr wrote: Hello, Can you run a job with qsub from your Galaxy server with your Galaxy user ? Thomas -- Thomas Bellembois, network and system administrator ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE +33 4 26 73 13 67 .The IGFL is a member of the portail-labos project (https://portail-labos.ens-lyon.fr/site/https://urldefense.proofpoint.com/v1/url?u=https://portail-labos.ens-lyon.fr/site/k=eEbcMSXJ22m%2Bwpc%2B3zaDpA%3D%3D%0Ar=%2FSzwK1QdKBgYgI1%2BE8ugS5x1w%2F01U44BllswL1jgZTE%3D%0Am=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0As=abdb53f74c8d32d1acef7a9c10af11da935baebac585dc803da3aff54b7b123a). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdochttps://urldefense.proofpoint.com/v1/url?u=http://itdoc.igfl.ens-lyon.fr/itdock=eEbcMSXJ22m%2Bwpc%2B3zaDpA%3D%3D%0Ar=%2FSzwK1QdKBgYgI1%2BE8ugS5x1w%2F01U44BllswL1jgZTE%3D%0Am=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0As=9978e8d2a1f01560f249e5439efff9f047338fa4fab2a1be17e5499555f224a9 On 21/01/2014 22:16, Cantarel, Brandi L. wrote: Hi all, I have been trying to set up my galaxy instance to use SGE -- I created a job_conf.xml using the sample as a model and updated the galaxy user bashrc with the DRMAA_LIBRARY_PATH export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so But when I try to add data to a library I get the error: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Not too comforting since I am the administrator. The error in the log says: galaxy.jobs.handler DEBUG 2014-01-21 14:57:39,478 (2) Dispatching to drmaa runner galaxy.jobs.handler ERROR 2014-01-21 14:57:39,479 put(): (2) Invalid job runner: drmaa What does that mean, Invalid job runner? Does this mean I have an error in my job_conf.xml? Here is my job_conf.xml ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=main tags=handlers/ /handlers destinations default=sge_default !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=sge_default runner=drmaa/ !-- Define parameters that are native to the job runner plugin. -- /destinations /job_conf Thanks for your help! ~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information. ___ 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/https://urldefense.proofpoint.com/v1/url?u=http://lists.bx.psu.edu/k=eEbcMSXJ22m%2Bwpc%2B3zaDpA%3D%3D%0Ar=%2FSzwK1QdKBgYgI1%2BE8ugS5x1w%2F01U44BllswL1jgZTE%3D%0Am=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0As=a2cdc2948a084286326cec83a2098ca7895e2a2d32d1cf8ecba9b573238927bb To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/https://urldefense.proofpoint.com/v1/url?u=http://galaxyproject.org/search/mailinglists/k=eEbcMSXJ22m%2Bwpc%2B3zaDpA%3D%3D%0Ar=%2FSzwK1QdKBgYgI1%2BE8ugS5x1w%2F01U44BllswL1jgZTE%3D%0Am=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0As=7132f6c2062cf27922c3decc299521acbd916e0ad877d0b83b5f359ec60e182a ___ 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
Re: [galaxy-dev] setting up the drmaa for sge
I may be wrong, but may be your : destination id=sge_default runner=drmaa/ parameter should be : destination id=sge_default runner=sge/ Here is my configuration file for example. ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ !-- SUN GRID ENGINE -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ /handlers destinations default=sge_default destination id=local runner=local/ destination id=sge_default runner=sge param id=nativeSpecification-b n/param /destination /destinations /job_conf Thomas On 22/01/2014 16:02, Cantarel, Brandi L. wrote: Are you asking if I can submit jobs to sge with the galaxy user on the server — yes, I can, at least I can on the command line... On Jan 22, 2014, at 3:00 AM, Thomas Bellembois thomas.bellemb...@ens-lyon.fr mailto:thomas.bellemb...@ens-lyon.fr wrote: Hello, Can you run a job with qsub from your Galaxy server with your Galaxy user ? Thomas -- Thomas Bellembois, network and system administrator ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE +33 4 26 73 13 67 .The IGFL is a member of the portail-labos project (https://portail-labos.ens-lyon.fr/site/). .IGFL IT documentation:http://itdoc.igfl.ens-lyon.fr/itdoc On 21/01/2014 22:16, Cantarel, Brandi L. wrote: Hi all, I have been trying to set up my galaxy instance to use SGE -- I created a job_conf.xml using the sample as a model and updated the galaxy user bashrc with the DRMAA_LIBRARY_PATH export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so But when I try to add data to a library I get the error: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Not too comforting since I am the administrator. The error in the log says: galaxy.jobs.handler DEBUG 2014-01-21 14:57:39,478 (2) Dispatching to drmaa runner galaxy.jobs.handler ERROR 2014-01-21 14:57:39,479 put(): (2) Invalid job runner: drmaa What does that mean, Invalid job runner? Does this mean I have an error in my job_conf.xml? Here is my job_conf.xml ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=main tags=handlers/ /handlers destinations default=sge_default !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=sge_default runner=drmaa/ !-- Define parameters that are native to the job runner plugin. -- /destinations /job_conf Thanks for your help! ~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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:
[galaxy-dev] XML wrapper : use cheetath variable in from_work_dir tag
Hello,
I don't know how to use a cheetah variable (#set var) inside a XML tag.
I mean when I try to do this :
#set foo = file.txt
...
outputs
data format=txt from_work_dir=something/${foo} name=test/
/outputs
from_work_dir tag contains something/${foo} instead of
something/file.txt
Is there a way to do this ?
Regards
Laure
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[galaxy-dev] XML wrapper : use cheetath variable in from_work_dir tag
Hello,
I don't know how to use a cheetah variable (#set var) inside a XML tag.
I mean when I try to do this :
#set foo = file.txt
...
outputs
data format=txt from_work_dir=something/${foo} name=test/
/outputs
from_work_dir tag contains something/${foo} instead of
something/file.txt
Is there a way to do this ?
Regards
Laure
___
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] small suggestion: customize stuff
Hello y'all I was wondering if I did the right thing : I've modified the file user.py to reset the user's password to a length of 8 characters by doing: diff /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/ARCHIVES/user.py_20140120_15.3.14 1092c1092 for i in range(7): --- for i in range(15): I believe the sys admin would like this to be customizable in the universe_wsgi.ini file. As well for the reset capability could be accessible just by the administrator. I would like to apologies to galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu if I'm spamming your email. Please let me know if I should remove this to my threads. Cordialement / Regards, Edgar Fernandez ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting up the drmaa for sge
That fixed it. Thanks a bunch! On Jan 22, 2014, at 9:27 AM, Thomas Bellembois thomas.bellemb...@ens-lyon.frmailto:thomas.bellemb...@ens-lyon.fr wrote: I may be wrong, but may be your : destination id=sge_default runner=drmaa/ parameter should be : destination id=sge_default runner=sge/ Here is my configuration file for example. ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ !-- SUN GRID ENGINE -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ /handlers destinations default=sge_default destination id=local runner=local/ destination id=sge_default runner=sge param id=nativeSpecification-b n/param /destination /destinations /job_conf Thomas On 22/01/2014 16:02, Cantarel, Brandi L. wrote: Are you asking if I can submit jobs to sge with the galaxy user on the server — yes, I can, at least I can on the command line... On Jan 22, 2014, at 3:00 AM, Thomas Bellembois thomas.bellemb...@ens-lyon.frmailto:thomas.bellemb...@ens-lyon.fr wrote: Hello, Can you run a job with qsub from your Galaxy server with your Galaxy user ? Thomas -- Thomas Bellembois, network and system administrator ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE +33 4 26 73 13 67 .The IGFL is a member of the portail-labos project (https://portail-labos.ens-lyon.fr/site/https://urldefense.proofpoint.com/v1/url?u=https://portail-labos.ens-lyon.fr/site/k=eEbcMSXJ22m%2Bwpc%2B3zaDpA%3D%3D%0Ar=%2FSzwK1QdKBgYgI1%2BE8ugS5x1w%2F01U44BllswL1jgZTE%3D%0Am=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0As=abdb53f74c8d32d1acef7a9c10af11da935baebac585dc803da3aff54b7b123a). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdochttps://urldefense.proofpoint.com/v1/url?u=http://itdoc.igfl.ens-lyon.fr/itdock=eEbcMSXJ22m%2Bwpc%2B3zaDpA%3D%3D%0Ar=%2FSzwK1QdKBgYgI1%2BE8ugS5x1w%2F01U44BllswL1jgZTE%3D%0Am=OVBvm1iGyH5TK3Bdxa4xpEWEoq3Rz3VQmUC%2FuDZemsQ%3D%0As=9978e8d2a1f01560f249e5439efff9f047338fa4fab2a1be17e5499555f224a9 On 21/01/2014 22:16, Cantarel, Brandi L. wrote: Hi all, I have been trying to set up my galaxy instance to use SGE -- I created a job_conf.xml using the sample as a model and updated the galaxy user bashrc with the DRMAA_LIBRARY_PATH export DRMAA_LIBRARY_PATH=/home/sge/lib/lx26-amd64/libdrmaa.so But when I try to add data to a library I get the error: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Not too comforting since I am the administrator. The error in the log says: galaxy.jobs.handler DEBUG 2014-01-21 14:57:39,478 (2) Dispatching to drmaa runner galaxy.jobs.handler ERROR 2014-01-21 14:57:39,479 put(): (2) Invalid job runner: drmaa What does that mean, Invalid job runner? Does this mean I have an error in my job_conf.xml? Here is my job_conf.xml ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=sge type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=main tags=handlers/ /handlers destinations default=sge_default !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=sge_default runner=drmaa/ !-- Define parameters that are native to the job runner plugin. -- /destinations /job_conf Thanks for your help! ~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information.
Re: [galaxy-dev] XML wrapper : use cheetath variable in from_work_dir tag
There is not a way to do this. The exact value of from_work_dir needs
to be known prior to evaluating the cheetah environment. If you need
to variably define the output location - my recommendation would be to
just drop form the from_work_dir attribute and append ; cp
something/${foo} $test to the end of your command - this copy has to
be done either way so I don't think this is any less efficient. Let me
know if this doesn't make sense and good luck!
-John
On Wed, Jan 22, 2014 at 2:37 AM, lquintri laure.quint...@ifremer.fr wrote:
Hello,
I don't know how to use a cheetah variable (#set var) inside a XML tag.
I mean when I try to do this :
#set foo = file.txt
...
outputs
data format=txt from_work_dir=something/${foo} name=test/
/outputs
from_work_dir tag contains something/${foo} instead of
something/file.txt
Is there a way to do this ?
Regards
Laure
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Re: [galaxy-dev] small suggestion: customize stuff
I have opened a small pull request to add this feature to galaxy-central. https://bitbucket.org/galaxy/galaxy-central/pull-request/307/allow-adjusting-the-reset-password-length/diff -John On Wed, Jan 22, 2014 at 8:31 AM, Fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello y’all I was wondering if I did the right thing : I’ve modified the file user.py to reset the user’s password to a length of 8 characters by doing: diff /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/ARCHIVES/user.py_20140120_15.3.14 1092c1092 for i in range(7): --- for i in range(15): I believe the sys admin would like this to be customizable in the universe_wsgi.ini file. As well for the reset capability could be accessible just by the administrator. I would like to apologies to galaxy-...@bx.psu.edu if I’m spamming your email. Please let me know if I should remove this to my threads. Cordialement / Regards, Edgar Fernandez ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Import workflows via API
Hi Neil,
can you retry after applying this commit from my new pull request?
https://bitbucket.org/nsoranzo/galaxy-central/commits/11597a078e6505087064315567ad3357c2d40c56
--
Nicola Soranzo
Bioinformatics Program, CRS4
Loc. Piscina Manna, 09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/
neil.burd...@csiro.au ha scritto:
Hi Nicola,
I've merged your changes into my version of the galaxy code
(slightly older than galaxy-central) I believe, however, I get the following
error when I try and execute your script:
Traceback (most recent call last):
File get_wfs.py, line 13, in module
common.post(api_key, 'http://barium-rbh:9100/extras/api/workflows/import',
data)
File /home/galaxy/milxcloud/scripts/api/common.py, line 48, in post
return simplejson.loads( urllib2.urlopen( req ).read() )
File /usr/lib/python2.7/urllib2.py, line 126, in urlopen
return _opener.open(url, data, timeout)
File /usr/lib/python2.7/urllib2.py, line 406, in open
response = meth(req, response)
File /usr/lib/python2.7/urllib2.py, line 519, in http_response
'http', request, response, code, msg, hdrs)
File /usr/lib/python2.7/urllib2.py, line 444, in error
return self._call_chain(*args)
File /usr/lib/python2.7/urllib2.py, line 378, in _call_chain
result = func(*args)
File /usr/lib/python2.7/urllib2.py, line 527, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
urllib2.HTTPError: HTTP Error 500: Internal Server Error
so I printed out the some lines in common.py
def post( api_key, url, data ):
# Do the actual POST.
url = make_url( api_key, url )
print URL is %s % url
URL is
http://barium-rbh:9100/extras/api/workflows/import?key=34ee80757f0d03de36e33a1676d245e4
the script is:
import sys
#sys.path.insert(1, 'milxcloud/scripts/api')
import common
api_key = '34ee80757f0d03de36e33a1676d245e4'
workflows = common.get(api_key,
'http://barium-rbh:9100/api/workflows?show_published=True')
print workflows
published_workflow_ids = [str(workflow[u'id']) for workflow in workflows if
bool(workflow[u'published'])]
print published_workflow_ids
for pw_id in published_workflow_ids:
data = {}
data['workflow_id'] = pw_id
common.post(api_key, 'http://barium-rbh:9100/extras/api/workflows/import',
data)
and I run it from ~/scripts/api
The output from the script is :
python get_wfs.py
[{'name': 'SUVR', 'tags': [], 'url': '/extras/api/workflows/f2db41e1fa331b3e',
'published': True, 'model_class': 'StoredWorkflow', 'id': 'f2db41e1fa331b3e'},
{'name': 'processSUVRData', 'tags': [], 'url':
'/extras/api/workflows/f597429621d6eb2b', 'published': True, 'model_class':
'StoredWorkflow', 'id': 'f597429621d6eb2b'}]
['f2db41e1fa331b3e', 'f597429621d6eb2b']
URL is
http://barium-rbh:9100/extras/api/workflows/import?key=34ee80757f0d03de36e33a1676d245e4
Any ideas why the import maybe failing?
Thanks
Neil
From: Nicola Soranzo [sora...@crs4.it]
Sent: Monday, January 20, 2014 9:03 PM
To: Burdett, Neil (CCI, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Import workflows via API
Hi Neil,
to import all published workflows you can use a script like this:
import sys
sys.path.insert(1, 'galaxy-central/scripts/api')
import common
api_key = 'YOUR_USER_API_KEY'
workflows = common.get(api_key,
'http://YOUR_SERVER/api/workflows?show_published=True')
published_workflow_ids = [str(workflow[u'id']) for workflow in
workflows if bool(workflow[u'published'])]
for pw_id in published_workflow_ids:
data['workflow_id'] = pw_id
common.post(api_key, 'http://YOUR_SERVER/api/workflows/import',
data)
Nicola
Il 2014-01-19 03:12 neil.burd...@csiro.au ha scritto:
Hi Nicola,
that is exactly what I'm looking for, however, how do
I execute the script/tool? I would like to import all published
workflows. What is the name of the script to run and the arguments ?
Can you give an example please?
Thanks again
Neil
Date: Fri, 17 Jan 2014 11:36:03 +0100
From: Nicola Soranzo sora...@crs4.it
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Import workflows via API
Message-ID: d834d247437269704a26e8bbf8f67...@crs4.it
Content-Type: text/plain; charset=UTF-8; format=flowed
Il 2014-01-17 06:45 neil.burd...@csiro.au ha scritto:
Hi,
I execute workflows via the API. However, if I want another user to
use my workflows, I can publish my workflows, but the new user then
has to go on to the web browser and import this workflow.
Is there a method/script which I can call via the API which can
import
all available (published) workflows so the user doesn't have to
click
a button on the web browser import workflow ?
Thanks for any help
Hi Neil,
you are very lucky, just yesterday my pull request implementing
exactly
this has been merged in galaxy-central:
Re: [galaxy-dev] XML wrapper : use cheetath variable in from_work_dir tag
Don’t think you need the { }
You may have to do something like this
#set foo = “file.txt
outputs
data format=txt from_work_dir=“something/#echo str ( $foo ) #
name=test/
/outputs
But try it just without the { }.
Cheetah is a bitch and note the spaces in the #echo str ( $foo ) # it seems to
be important to have them there
Regards,
Thon
[cid:enz_logo_2_new36d101]
Thon deBoer
Director of Software
3415 Colorado Ave.
Room A255
Boulder, CO 80303
Cell: (650) 799-6839
tdeb...@enzymatics.com
www.enzymatics.com
Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments are
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for the individual(s) to whom it is addressed, and may not be saved, copied,
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notify the sender by e-mail.
On Jan 22, 2014, at 7:58 AM, lquintri
laure.quint...@ifremer.frmailto:laure.quint...@ifremer.fr wrote:
Hello,
I don't know how to use a cheetah variable (#set var) inside a XML tag.
I mean when I try to do this :
#set foo = file.txt
...
outputs
data format=txt from_work_dir=something/${foo} name=test/
/outputs
from_work_dir tag contains something/${foo} instead of something/file.txt
Is there a way to do this ?
Regards
Laure
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