Re: [galaxy-dev] condor jobs
On Fri, Jan 30, 2015 at 9:24 AM, Shrum, Donald C dcsh...@admin.fsu.edu wrote: Hi all, I’ve configured one of our tools to submit jobs to our condor cluster. I can see the job is routed to the condor runner: == handler4.log == galaxy.jobs.handler DEBUG 2015-01-30 09:14:58,092 (508) Dispatching to condor runner galaxy.jobs DEBUG 2015-01-30 09:14:58,204 (508) Persisting job destination (destination id: condor) I can see that indeed the job is submitted to the condor cluster: [root@galaxy galaxy-dist]# condor_q -- Submitter: galaxy.local : 10.177.61.90:55265 : galaxy.local ID OWNERSUBMITTED RUN_TIME ST PRI SIZE CMD 21.0 galaxy 1/30 09:15 0+00:00:02 R 0 0.0 galaxy_509.sh The job begins to run: == handler4.log == galaxy.jobs.runners.condor DEBUG 2015-01-30 09:15:03,827 (508/20) job is now running galaxy.jobs.runners.condor DEBUG 2015-01-30 09:15:05,183 (508/20) job has completed Galaxy is almost immediately removing the job working directory: Here is a snippet of the errors: == handler4.log == galaxy.jobs.runners DEBUG 2015-01-30 09:15:06,372 (508/20) Unable to cleanup /panfs/storage.local/opt/galaxy-dist/database/pbs/galaxy_508.ec: [Errno 2] No such file or directory: '/panfs/storage.local/opt/galaxy-dist/database/pbs/galaxy_508.ec' galaxy.jobs DEBUG 2015-01-30 09:15:06,816 setting dataset state to ERROR galaxy.datatypes.metadata DEBUG 2015-01-30 09:15:06,996 Failed to cleanup MetadataTempFile temp files from /panfs/storage.local/galaxy-data/job_working_directory/000/508/metadata_out_HistoryDatasetAssociation_717_zrzVqh: No JSON object could be decoded Is it possible galaxy is attempting to query condor and see if the job is running, not finding anything and deciding that the job is not running and bailing out? I’ve reconstructed the process step by step using the logs but I have not been able to see exactly where the condor_submit command is shown so I can try to submit the same job manually. Does anyone have a suggestion for debugging this? Two most relevant files would be: https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/jobs/runners/condor.py https://bitbucket.org/galaxy/galaxy-central/src/tip/lib/galaxy/jobs/runners/util/condor/__init__.py The condor job logic strikes me as pretty brittle - it has always worked for me when I have tested it but given how it is readiing logs I would imagine very small changes to condor might cause it to fail. So one thing to check is summarize_condor_log in lib/galaxy/jobs/runners/util/condor/__init__.py - to see if that logic matches the way your condor produces log files. Given the symptoms - it might be also worth just sleeping for 5 seconds in condor_submit in lib/galaxy/jobs/runners/util/condor/__init__.py and then verifying that Galaxy is actually properly parsing the correct external id. Here is an untested diff that adds the sleep and some more log statements that might help: https://gist.github.com/jmchilton/d0afd7242370642d5b43 If you are able to fix the problem - please let us know how so we can fix it upstream. -John Thanks, Don Florida State University Research Computing Center ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Tests failing with Exception: History in error state.
Hi Dannon, Nicola, This sounds very promising - I'll rerun the TravisCI job and we can expect it to work this time :) https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d (half an hour ago!) When will this reach the Tool Shed and Test Tool Shed? The upload job failure seems to be the root cause of many of the unexpected test failures. Thanks, Peter On Fri, Jan 30, 2015 at 5:19 PM, Dannon Baker dannon.ba...@gmail.com wrote: Yep, the FutureWarning that that commit resolves would have caused the upload job to end up as an error; I'm betting this is what was causing Peter's issues too. On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo nsora...@tiscali.it wrote: Hi Peter, I was also getting Exception: History in error state errors with BioBlend continuous integration testing, but those seem to be fixed with latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d . Nicola Il 30.01.2015 17:36 Peter Cock ha scritto: Retitling thread, On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: Exception: History in error state. I'm sure you'll learn more once you look over the logs, Thank you, Peter Right now the mummer example given above is passing, but I am still getting this error on some of my tools, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go tested 2015-01-25 11:21:12 https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss tested 2015-01-25 10:52:03 (Many of my other tools are also currently listed with different unexpected failures, some of which include the Exception: History in error state. traceback.) Interestingly, I've just got what appears to be the same exception from a TravisCI test run (following a trivial change to README files): https://travis-ci.org/peterjc/galaxy_blast/builds/48893916 e.g. (one of many similar failing tests in this log) == ERROR: test_tool_00 (functional.test_toolbox.TestForTool_blastxml_to_top_descr) BLAST top hit descriptions ( blastxml_to_top_descr ) Test-1 -- Traceback (most recent call last): File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py, line 268, in test_tool self.do_it( td ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py, line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 42, in stage_data_in_history upload_wait() File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 279, in wait while not self.__history_ready( history_id ): File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 297, in __history_ready return self._state_ready( state, error_msg=History in error state. ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 356, in _state_ready raise Exception( error_msg ) Exception: History in error state. I do not recall seeing this problem locally when using my development instllation of galaxy-central. The TravisCI failure suggests this could be a stochastic resource contention (I can re-run the TravisCI build and see if this works second time round?), which is more prone to fail under the Tool Shed framework? 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the
Re: [galaxy-dev] tool shed updates broken on my local server
Hi Anne,
moving the whole Galaxy installation is a tough job and we do not really
have a good process for it. Your problem is most probably caused by the
inconsistency in the DB. The path to the shed_tool_conf.xml is stored there
and the changes you made to the location of the installation did not
propagate there.
Please have a look at the following script that Dave B. made:
https://gist.github.com/InitHello/d208cd056baf088aca1f
This script will soon be part of the distribution (in /scripts) and should
help you solving your issues.
Thank you for using Galaxy.
Martin, Galaxy Team
On Thu Jan 29 2015 at 11:47:19 AM Anne Pajon anne.pa...@cruk.cam.ac.uk
wrote:
Hi there,
I am currently trying to migrate our Galaxy production server onto new
hardware and I am facing many challenges. Recently I've been unable to
update tools from the tool shed. During the migration I've moved across the
files, the data, the tools and their dependencies as well as the database.
But I am getting this error while trying to update any tools that are
marked 'Updates are available in the Tool Shed for this revision' from the
GUI: Admin Manage installed tool shed repositories fasta_formatter menu
Get updates:
Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
The error has been logged to our team.
Here is the log from paster.log:
10.20.13.16 - - [29/Jan/2015:16:43:45 +0100] GET
/admin_toolshed/update_to_changeset_revision?tool_shed_url=
https://toolshed.g2.bx.psu.edu/name=fasta_formatter;
owner=devteamchangeset_revision=8f0ae92440b8latest_changeset_revision=
1dbb5181c327latest_ctx_rev=1 HTTP/1.1 500 - http://bioinf-gal001:8080/
admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_
checkboxes=falseadvanced_search=falsef-deleted=False
f-free-text-search=fasta_formatter Mozilla/5.0 (Macintosh; Intel Mac OS
X 10.8; rv:35.0) Gecko/20100101 Firefox/35.0
Error - type 'exceptions.AttributeError': 'NoneType' object has no
attribute 'get'
URL: http://bioinf-gal001:8080/admin_toolshed/update_to_
changeset_revision?tool_shed_url=https://toolshed.g2.bx.
psu.edu/name=fasta_formatterowner=devteamchangeset_
revision=8f0ae92440b8latest_changeset_revision=
1dbb5181c327latest_ctx_rev=1
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py',
line 87 in decorator
return func( self, trans, *args, **kwargs )
File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/webapps/
galaxy/controllers/admin_toolshed.py', line 1953 in
update_to_changeset_revision
persist=True )
File '/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/galaxy_
install/metadata/installed_repository_metadata_manager.py', line 31 in
__init__
metadata_dict=metadata_dict, user=None )
File
'/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py',
line 60 in __init__
self.metadata_dict = { 'shed_config_filename' :
self.shed_config_dict.get( 'config_filename', None ) }
AttributeError: 'NoneType' object has no attribute 'get'
CGI Variables
-
CONTENT_LENGTH: '0'
HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;
q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a44ec9cad39b012
02307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9'
HTTP_HOST: 'bioinf-gal001:8080'
HTTP_REFERER: 'http://bioinf-gal001:8080/admin_toolshed/browse_
repositories?async=falsesort=namepage=1show_item_
checkboxes=falseadvanced_search=falsef-deleted=False
f-free-text-search=fasta_formatter'
HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:35.0)
Gecko/20100101 Firefox/35.0'
PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
QUERY_STRING: 'tool_shed_url=https://toolshed.g2.bx.psu.edu/name=
fasta_formatterowner=devteamchangeset_revision=
8f0ae92440b8latest_changeset_revision=1dbb5181c327latest_ctx_rev=1'
REMOTE_ADDR: '10.20.13.16'
REQUEST_METHOD:
Re: [galaxy-dev] Pulsar on a remote (SGE) cluster
On Thu, Jan 29, 2015 at 4:43 PM, Joseph Brent Greer joseph.gr...@northwestern.edu wrote: Hi all, We have Pulsar working in a synchronous fashion using RESTful services on our local network. Now, we’re trying to use Pulsar on a remote (SGE) cluster and we will not have the ability to mount a shared file system. What is the best way to use Galaxy to queue jobs? Having a shared file system is definitely the best way to go if at all possible. If you definitely cannot make that happen - than Pulsar is probably the way to go - but it has limitations - it cannot for instance leverage tool shed installed dependencies and it certainly doesn't scale as well as Galaxy itself yet. I am working on these problems and am happy to help work through the problems you encounter - but I just like to throw out the warning about Pulsar. If Pulsar is the answer, how do we defer to the cluster’s queue and have Pulsar wait on it? So it sounds like you have experience setting up Pulsar - you will now need to set it up one a node connected to the remote cluster and open a port for it (unless you want to setup a message queue - but I recommend the RESTful mode when possible - it seems more robust currently). Once you have Pulsar setup - you will need to configure it to talk to your SGE cluster. For that you will need to install an SGE drmaa library on the node (it may already be available). Then copy local_env.sh.sample to local_env.sh in Pulsar and setup DRMAA_LIBRARY_PATH. export DRMAA_LIBRARY_PATH=/path/to/your/libdrmaa.so and finally setup a job_managers.ini file (cp job_managers.ini.sample job_managers.ini) and change the default section to something like: [manager:_default_] type=queued_drmaa More information about configuring job managers here https://pulsar.readthedocs.org/en/latest/job_managers.html. Finally - you need to configure Galaxy to use the correct Pulsar job runner - it might look something like this - https://gist.github.com/jmchilton/ca39ef1a3241d9074121. That should be it - and then Galaxy should send jobs to the cluster as needed. How should Pulsar notify Galaxy when multiple jobs are done running? Galaxy will poll the remote Pulsar server to determine when the jobs are complete. If you cannot open a port for pulsar to do this polling - then you will need to setup a message queue and then configure both sides to use that - I would definitely try to bully your cluster admins into opening that port before resorting to that though. We’ve looked through the documentation and listservs and haven’t found anything directly related. Pulsar was previously called the LWR - so there are more conversations related to it on galaxy-dev referring to it as the LWR. Any help or suggestions would be great. Hopefully this helps and good luck! -John Thanks, Joe Greer Proteomics Center of Excellence Northwestern University ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool Tests failing with Exception: History in error state.
Retitling thread, On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: Exception: History in error state. I'm sure you'll learn more once you look over the logs, Thank you, Peter Right now the mummer example given above is passing, but I am still getting this error on some of my tools, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go tested 2015-01-25 11:21:12 https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss tested 2015-01-25 10:52:03 (Many of my other tools are also currently listed with different unexpected failures, some of which include the Exception: History in error state. traceback.) Interestingly, I've just got what appears to be the same exception from a TravisCI test run (following a trivial change to README files): https://travis-ci.org/peterjc/galaxy_blast/builds/48893916 e.g. (one of many similar failing tests in this log) == ERROR: test_tool_00 (functional.test_toolbox.TestForTool_blastxml_to_top_descr) BLAST top hit descriptions ( blastxml_to_top_descr ) Test-1 -- Traceback (most recent call last): File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py, line 268, in test_tool self.do_it( td ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py, line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 42, in stage_data_in_history upload_wait() File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 279, in wait while not self.__history_ready( history_id ): File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 297, in __history_ready return self._state_ready( state, error_msg=History in error state. ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 356, in _state_ready raise Exception( error_msg ) Exception: History in error state. I do not recall seeing this problem locally when using my development instllation of galaxy-central. The TravisCI failure suggests this could be a stochastic resource contention (I can re-run the TravisCI build and see if this works second time round?), which is more prone to fail under the Tool Shed framework? 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Tests failing with Exception: History in error state.
Yep, the FutureWarning that that commit resolves would have caused the upload job to end up as an error; I'm betting this is what was causing Peter's issues too. On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo nsora...@tiscali.it wrote: Hi Peter, I was also getting Exception: History in error state errors with BioBlend continuous integration testing, but those seem to be fixed with latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d . Nicola Il 30.01.2015 17:36 Peter Cock ha scritto: Retitling thread, On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: Exception: History in error state. I'm sure you'll learn more once you look over the logs, Thank you, Peter Right now the mummer example given above is passing, but I am still getting this error on some of my tools, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go tested 2015-01-25 11:21:12 https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss tested 2015-01-25 10:52:03 (Many of my other tools are also currently listed with different unexpected failures, some of which include the Exception: History in error state. traceback.) Interestingly, I've just got what appears to be the same exception from a TravisCI test run (following a trivial change to README files): https://travis-ci.org/peterjc/galaxy_blast/builds/48893916 e.g. (one of many similar failing tests in this log) == ERROR: test_tool_00 (functional.test_toolbox.TestForTool_blastxml_to_top_descr) BLAST top hit descriptions ( blastxml_to_top_descr ) Test-1 -- Traceback (most recent call last): File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py, line 268, in test_tool self.do_it( td ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py, line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 42, in stage_data_in_history upload_wait() File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 279, in wait while not self.__history_ready( history_id ): File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 297, in __history_ready return self._state_ready( state, error_msg=History in error state. ) File /home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py, line 356, in _state_ready raise Exception( error_msg ) Exception: History in error state. I do not recall seeing this problem locally when using my development instllation of galaxy-central. The TravisCI failure suggests this could be a stochastic resource contention (I can re-run the TravisCI build and see if this works second time round?), which is more prone to fail under the Tool Shed framework? 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?
On Fri Jan 30 2015 at 5:36:29 AM Peter Cock https://toolshed.g2.bx.psu.edu/repository/get_functional_ test_rss?owner=peterjcstatus=all Internal Server Error ... Trello issue logged, https://trello.com/c/ZOW0NPzb/2378-main-toolshed-rss-feed- for-test-results-offline Also still broken. This is the same error from the test toolshed, and this will be fixed with the next main toolshed server update that includes Dave's patch. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?
On Fri, Jan 30, 2015 at 2:07 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Fri Jan 30 2015 at 5:36:29 AM Peter Cock https://toolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjcstatus=all Internal Server Error ... Trello issue logged, https://trello.com/c/ZOW0NPzb/2378-main-toolshed-rss-feed-for-test-results-offline Also still broken. This is the same error from the test toolshed, and this will be fixed with the next main toolshed server update that includes Dave's patch. Thanks Dannon, Should I start filing bugs for the specific classes of unexpected tool test failures? e.g. Exception: History in error state. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] data sharing without duplication?
Good morning Gents, I hope everyone is well. I was wondering if it's possible to share data on Galaxy without all the users downloading the data to their history. Let me explain, teachers will be sharing data with their students. And the students will need to work with that specific data. However, I would like them to be able to read that data without replicating it on their history. Is that possible? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] data sharing without duplication?
Bjoern's answer is a good one. Another way we commonly do this is by preparing a 'base' history published with the datasets the students need to get started -- something like https://usegalaxy.org/u/mimi31k/h/chip-seq-example-1-raw-data. Students then click a single button to import that history and start working with it. To be clear, there is no actual duplication of data using either this or the data libraries approach. On Fri Jan 30 2015 at 9:33:58 AM Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Edgar, this is indeed possible. Please have a look at Galaxy data libraries: https://wiki.galaxyproject.org/Admin/DataLibraries/Libraries Cheers, Bjoern Am 30.01.2015 um 15:30 schrieb Fernandez Edgar: Good morning Gents, I hope everyone is well. I was wondering if it's possible to share data on Galaxy without all the users downloading the data to their history. Let me explain, teachers will be sharing data with their students. And the students will need to work with that specific data. However, I would like them to be able to read that data without replicating it on their history. Is that possible? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
