[galaxy-dev] GCC2013 Talk Abstract Submission closes this Friday
Hello all, This is a final reminder that the *deadline for submitting an oral presentation abstract is this 12 April, this Friday*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. And in case you missed the announcement about GIgaScience and GCC2013 talks: We are pleased to announce that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience http://www.gigasciencejournal.com/* and that BGIhttp://www.genomics.cn/en/indexwill generously cover the article processing fees for these articles. See the announcement http://wiki.galaxyproject.org/News/GigaScienceGalaxyCFPfor details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements cleme...@galaxyproject.orgwrote: Dear Galaxy Community, We are pleased to announce that early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register and paper and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are now open for the 2013 Galaxy Community Conference (GCC2013)http://wiki.galaxyproject.org/Events/GCC2013 . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo http://uio.no/. GCC2013 http://wiki.galaxyproject.org/Events/GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register * *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2013/Organizers PS: And please help get the word outhttp://wiki.galaxyproject.org/Events/GCC2013/Promotion ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] How to distribute our local installation via git(logistics)
Hello, We want to able to distribute Galaxy configured with the UCSC browser, specially for people who are not too UNIX savvy. We had a question on how to do this, since we are planning to do it via git. How can we set up the git server, in such a way that it doesn't compromise important files that are specific to our installation. For example, in our universe_wsgi.ini file we have passwords for our database that we do not want to distribute. However, we do want to distribute universe_wsgi.ini in releases so people can be updated in important changes. We were thinking that maybe we should have a test machine to make sure all the changes does not break Galaxy, and then push the changes to our server machine an to our git server. However, we are not sure if this is the most efficient way to do it. Does anyone know how we can accomplish this without complicating too many things? Thank you for your time and patience, --Ricardo Perez ___ 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] Custom tool need a directory as input
Hi David, tha BAM file is compressed in the BGZF format and is not uncompressed by default. So I would try the following: - write your own datatype http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes - write a sniffer similar to the BAM sniffer https://bitbucket.org/galaxy/galaxy-central/src/8fc56b85e0a5353ffd6790685a4a7d8a84938409/lib/galaxy/datatypes/binary.py Thanks to the wonderful toolshed it is also possible to include datatypes in your repo. http://wiki.galaxyproject.org/ToolShedDatatypesFeatures Hopefully that will work out! Bjoern Hello, I have a tool that needs a directory containing a bunch of files as an input : mytool -d $directory -p param1 -o $output ... I thought the best approach would be to use a Zip file that I would temporally uncompress in a bash wrapper. But when I upload the zip file, galaxy unzip it. What would you recommend to accomplish such a task ? I want that tool to be installable from a toolshed, so I don't want to modify the upload.py script or any other files. Thanks, David ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ 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] setup grid engine
On Apr 8, 2013, at 9:24 PM, Jingzhi Zhu wrote: Hi Nate, That's it! After I made that change, I was able to see jobs are successfully submitted to the SGE queue and then run. So this is great! I now run into another issue. galaxy.jobs.runners.drmaa DEBUG 2013-04-08 21:16:56,386 (15/530948) state change: job finished, but failed galaxy.jobs.runners ERROR 2013-04-08 21:16:56,526 (15/530948) Job output not returned from cluster: [Errno 2] No such file or directory: '/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o' galaxy.jobs DEBUG 2013-04-08 21:16:56,559 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-04-08 21:16:56,603 setting dataset state to ERROR galaxy.jobs DEBUG 2013-04-08 21:16:56,796 job 15 ended Google search shows a lot of similar errors, but it is never clear how to resolve it. When this job is run, qstat -j shows the following stderr_path_list: NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.e stdout_path_list: NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o script_file: /net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.sh I can see the galaxy_15.sh exists in the above directory, but the galaxy_15.o and galaxy_15.e do not exist during the job run. Where are those files saved? Do you have any idea how to fix it? Thank you so much! Hi Jingzhi, Please use reply all to keep replies on the list. Does that directory exist on the cluster? A shared filesystem mounted at the same path is (currently) required between Galaxy and the cluster. --nate Jingzhi On Apr 8, 2013, at 4:46 PM, Nate Coraor wrote: Hi Jingzhi, Unfortunately, there's a mistake in the sample config for that runner plugin, the line to load the plugin should be: plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ The sample config was fixed in a later commit to the stable branch, and seeing as there was a security release today I would suggest just updating your Galaxy installation to the latest stable commit anyway: % hg pull % hg update stable --nate On Apr 8, 2013, at 4:14 PM, Jingzhi Zhu wrote: I have downloaded the 04_01 release and tried to configure the Sun Grid Engine so that the job can run on our cluster. I have export the DRMAA_LIBRARY_PATH environment variable (export DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on the plugins section so it looks like this in job_conf.xml 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=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAARunner/ /plugins The run.sh returns the following error galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 37, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/app.py, line 159, in __init__ self.job_manager = manager.JobManager( self ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/manager.py, line 31, in __init__ self.job_handler = handler.JobHandler( app ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 543, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins() File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 476, in get_job_runner_plugins runner_class = getattr( module, class_name ) AttributeError: 'module' object has no attribute 'DRMAARunner' Can someone point to me what is going on here? If you have configured the SGE successfully with the latest 4.1 release, can
Re: [galaxy-dev] How to test DRMAA configuration?
On Apr 9, 2013, at 1:38 AM, Joshua Orvis wrote: It has been a while, but checking in again for any possible solution or advice where to look here? On Tue, Feb 26, 2013 at 10:06 AM, Joshua Orvis jor...@gmail.com wrote: Thanks for your response. That seemed to work, to a point. I redid the same FASTQ-FASTA conversion test and could see using command-line utilities that the job started on the grid (SGE is behind it.) About 10 minutes have gone by though since the job stopped running on the grid and the interface is still spinning as if it's running. I checked the Galaxy log for that job ID and I see these entries: galaxy.jobs.runners.drmaa INFO 2013-02-26 10:51:15,670 (103) queued as 5224332 galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:51:16,390 (103/5224332) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:51:30,422 (103/5224332) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:52:32,623 (103/5224332) is still in running state, adding to the DRM queue galaxy.jobs.runners.drmaa DEBUG 2013-02-26 10:54:31,961 (103/5224332) job left DRM queue with following message: code 18: The job specified by the 'jobid' does not exist. The SGE qacct utility for that job shows me that it took 3.5 minutes to run and that the return status was 0, so it executed successfully. It seems that Galaxy is missing the completion event for the job? Hi Joshua, The job should have completed eventually, Galaxy may be have spent a long time setting metadata on the job outputs, which would explain why it appears to finish but does not. Have you set `set_metadata_externally = True` in universe_wsgi.ini? --nate Joshua On Tue, Feb 26, 2013 at 12:17 AM, Ross ross.laza...@gmail.com wrote: See if adding the default queue name to the job runner path - eg: default_cluster_job_runner = drmaa:///default works any better? Galaxy will default to the local runner if it can't find the nominated drmaa path AFAIK and I don't think 'default' is the default :) On Tue, Feb 26, 2013 at 4:51 PM, Joshua Orvis jor...@gmail.com wrote: I have a working local Galaxy instance and wanted to enable DRMAA support to utilize our SGE (or LSF) grid. Following the guide here I set what I appeared to need to make this work. From the DRMAA_LIBRARY_PATH env variable to all the configuration settings in universe_wsgi.ini, reconfiguring the server hosting Galaxy as a submit host, etc. Some specific config file changes made: new_file_path = /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/tmp start_job_runners = drmaa default_cluster_job_runner = drmaa:/// set_metadata_externally = True outputs_to_working_directory = True I then killed and restarted the Galaxy instance and tried a simple FASTQ - FASTA test execution, but it ran locally. I couldn't find any sort of errors or messages related to DRMAA in the server log, and the job ran to completion. I commented out the local tool runner overrides. What can I do to test my DRMAA configuration and where should I look for errors? Thanks - Joshua ___ 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/ 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/
Re: [galaxy-dev] galaxy local installation
On Apr 8, 2013, at 5:01 PM, Yinan Wan wrote:
Hi,
I was trying to install the galaxy on my laptop and run into the following
error
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 345, in resolve
egg.resolve()
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File build/bdist.linux-i686/egg/pkg_resources.py, line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.
Because I have numpy installed which seems to be conflict to galaxy, so I was
install with virtual python environment (virtualenv), and also tried the
protection environment provided in the galaxy instruction page
(http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer),
and both came across the same error as indicated above.
Some information you may be interested:
(GalaxyENV)yinan@Macbook galaxy-dist$ python -V
Python 2.7.3
(GalaxyENV)yinan@Macbook galaxy-dist$ python scripts/get_platforms.py
macosx-10.7-x86_64-ucs2
It will be great if you can help me out.
Hi Yinan,
This is surprising, virtualenv should have resolved the conflict(s). Did you
use the --no-site-packages option when you created the env?
Also, you may be able to simply run fetch_eggs.py a second time and have it
succeed in fetching the dependency.
--nate
Thanks,
Yinan
--
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] setup grid engine
Hi Nate, Yes, the directory does exist in the NFS share. I can see galaxy_15.sh exists in this directory, but not the galaxy_15.o and galaxy_15.e file. $ ls -l /net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/ total 129 -rwxrwxr-x 1 love-galaxy love-galaxy 1889 Apr 8 21:15 galaxy_15.sh -rwxrwx--- 1 love-galaxy love-galaxy 2543 Apr 8 21:15 metadata_in_HistoryDatasetAssociation_15_cJgqA4 -rwxrwx--- 1 love-galaxy love-galaxy 20 Apr 8 21:15 metadata_kwds_HistoryDatasetAssociation_15_KHQqa8 -rwxrwx--- 1 love-galaxy love-galaxy0 Apr 8 21:15 metadata_out_HistoryDatasetAssociation_15_CztZ4c -rwxrwx--- 1 love-galaxy love-galaxy2 Apr 8 21:15 metadata_override_HistoryDatasetAssociation_15_3UAQKB -rwxrwx--- 1 love-galaxy love-galaxy 41 Apr 8 21:15 metadata_results_HistoryDatasetAssociation_15_vvt6Jv Thanks, Jingzhi On Apr 9, 2013, at 8:25 AM, Nate Coraor wrote: On Apr 8, 2013, at 9:24 PM, Jingzhi Zhu wrote: Hi Nate, That's it! After I made that change, I was able to see jobs are successfully submitted to the SGE queue and then run. So this is great! I now run into another issue. galaxy.jobs.runners.drmaa DEBUG 2013-04-08 21:16:56,386 (15/530948) state change: job finished, but failed galaxy.jobs.runners ERROR 2013-04-08 21:16:56,526 (15/530948) Job output not returned from cluster: [Errno 2] No such file or directory: '/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o' galaxy.jobs DEBUG 2013-04-08 21:16:56,559 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-04-08 21:16:56,603 setting dataset state to ERROR galaxy.jobs DEBUG 2013-04-08 21:16:56,796 job 15 ended Google search shows a lot of similar errors, but it is never clear how to resolve it. When this job is run, qstat -j shows the following stderr_path_list: NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.e stdout_path_list: NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o script_file: /net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.sh I can see the galaxy_15.sh exists in the above directory, but the galaxy_15.o and galaxy_15.e do not exist during the job run. Where are those files saved? Do you have any idea how to fix it? Thank you so much! Hi Jingzhi, Please use reply all to keep replies on the list. Does that directory exist on the cluster? A shared filesystem mounted at the same path is (currently) required between Galaxy and the cluster. --nate Jingzhi On Apr 8, 2013, at 4:46 PM, Nate Coraor wrote: Hi Jingzhi, Unfortunately, there's a mistake in the sample config for that runner plugin, the line to load the plugin should be: plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ The sample config was fixed in a later commit to the stable branch, and seeing as there was a security release today I would suggest just updating your Galaxy installation to the latest stable commit anyway: % hg pull % hg update stable --nate On Apr 8, 2013, at 4:14 PM, Jingzhi Zhu wrote: I have downloaded the 04_01 release and tried to configure the Sun Grid Engine so that the job can run on our cluster. I have export the DRMAA_LIBRARY_PATH environment variable (export DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on the plugins section so it looks like this in job_conf.xml 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=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAARunner/ /plugins The run.sh returns the following error galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 37, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/app.py, line 159, in __init__ self.job_manager = manager.JobManager( self ) File
Re: [galaxy-dev] How to be an admin?
That does not help. Actually, I tried to change random things in the universe_wsgi.ini, like setting the port to 8081, but none of the changes take effect when I restart the server. I am confused... - Original Message - From: Peter Cock p.j.a.c...@googlemail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: galaxy-dev@lists.bx.psu.edu Date: 2013-04-07 23:28:31 Subject: Re: [galaxy-dev] How to be an admin? On Sun, Apr 7, 2013 at 1:27 PM, Tobias Hohenaur hohena...@brain.riken.jp wrote: Hello, I just installed and updated a local instance of Galaxy on my mac. I then created a user and set the according username (email) as admin in the universe_wsgi.ini file. When I save and restart the server no admin panel appears. What am I doing wrong? Thank you very much for your help! Tobias Make sure you are logged in, and that the email address of your Galaxy account matches the universe_wsgi.ini setting exactly (case may be important). Also the setting used to have problems with extra white space (but I think that was fixed). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to be an admin?
How is it that you're restarting the server? It might be useful to check galaxy's log to see what's going on -- this would be paster.log in your galaxy directory or perhaps the foreground of the terminal you're executing galaxy from. -Dannon On Tue, Apr 9, 2013 at 9:25 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: That does not help. Actually, I tried to change random things in the universe_wsgi.ini, like setting the port to 8081, but none of the changes take effect when I restart the server. I am confused... - Original Message - From: Peter Cock p.j.a.c...@googlemail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: galaxy-dev@lists.bx.psu.edu Date: 2013-04-07 23:28:31 Subject: Re: [galaxy-dev] How to be an admin? On Sun, Apr 7, 2013 at 1:27 PM, Tobias Hohenaur hohena...@brain.riken.jp wrote: Hello, I just installed and updated a local instance of Galaxy on my mac. I then created a user and set the according username (email) as admin in the universe_wsgi.ini file. When I save and restart the server no admin panel appears. What am I doing wrong? Thank you very much for your help! Tobias Make sure you are logged in, and that the email address of your Galaxy account matches the universe_wsgi.ini setting exactly (case may be important). Also the setting used to have problems with extra white space (but I think that was fixed). 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/ 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/
Re: [galaxy-dev] How to be an admin?
I just hit ctrl c in the terminal to stop. Is that enough? - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:30:38 Subject: Re: [galaxy-dev] How to be an admin? How is it that you're restarting the server? It might be useful to check galaxy's log to see what's going on -- this would be paster.log in your galaxy directory or perhaps the foreground of the terminal you're executing galaxy from. -Dannon On Tue, Apr 9, 2013 at 9:25 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: That does not help. Actually, I tried to change random things in the universe_wsgi.ini, like setting the port to 8081, but none of the changes take effect when I restart the server. I am confused... - Original Message - From: Peter Cock p.j.a.c...@googlemail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: galaxy-dev@lists.bx.psu.edu Date: 2013-04-07 23:28:31 Subject: Re: [galaxy-dev] How to be an admin? On Sun, Apr 7, 2013 at 1:27 PM, Tobias Hohenaur hohena...@brain.riken.jp wrote: Hello, I just installed and updated a local instance of Galaxy on my mac. I then created a user and set the according username (email) as admin in the universe_wsgi.ini file. When I save and restart the server no admin panel appears. What am I doing wrong? Thank you very much for your help! Tobias Make sure you are logged in, and that the email address of your Galaxy account matches the universe_wsgi.ini setting exactly (case may be important). Also the setting used to have problems with extra white space (but I think that was fixed). 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/ 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/
Re: [galaxy-dev] How to be an admin?
Thank you for hinting the reload option. I opened the universe_wsgi.ini in the galaxy-dist folder and changed the port to 8081, the host to 0.0.0.0, then saved. The server reloads, but the changes have not taken effect. It is still at 127.0.0.1 and 8080... As far as I can see there is no other universe_wsgi.ini file except one that is calles universe_wsgi.ini sample. - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:47:04 Subject: Re: [galaxy-dev] How to be an admin? Yeah, if you're running it with just `run.sh`, that should work fine. One thing you can do if you're going to be tweaking a bunch of settings would be to run it with the reload option enabled `run.sh --reload`. When you change the port in universe_wsgi.ini in the galaxy directory, kill the server and restart, in the log at the end you should see something like: serving on 0.0.0.0:new port view at http://127.0.0.1:new port If you're not seeing that, I'd verify that you're editing the correct universe_wsgi.ini. Perhaps you have multiple galaxies installed somehow? On Tue, Apr 9, 2013 at 9:39 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: I just hit ctrl c in the terminal to stop. Is that enough? - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:30:38 Subject: Re: [galaxy-dev] How to be an admin? How is it that you're restarting the server? It might be useful to check galaxy's log to see what's going on -- this would be paster.log in your galaxy directory or perhaps the foreground of the terminal you're executing galaxy from. -Dannon On Tue, Apr 9, 2013 at 9:25 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: That does not help. Actually, I tried to change random things in the universe_wsgi.ini, like setting the port to 8081, but none of the changes take effect when I restart the server. I am confused... - Original Message - From: Peter Cock p.j.a.c...@googlemail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: galaxy-dev@lists.bx.psu.edu Date: 2013-04-07 23:28:31 Subject: Re: [galaxy-dev] How to be an admin? On Sun, Apr 7, 2013 at 1:27 PM, Tobias Hohenaur hohena...@brain.riken.jp wrote: Hello, I just installed and updated a local instance of Galaxy on my mac. I then created a user and set the according username (email) as admin in the universe_wsgi.ini file. When I save and restart the server no admin panel appears. What am I doing wrong? Thank you very much for your help! Tobias Make sure you are logged in, and that the email address of your Galaxy account matches the universe_wsgi.ini setting exactly (case may be important). Also the setting used to have problems with extra white space (but I think that was fixed). 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/ 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/
Re: [galaxy-dev] GalaxyAdmins Group: Future Directions?
Hi Hans, Thanks for the response. I didn't mean to advocate for an overlapping group but rather to identify means to strengthen the existing dev and user group interactions. There might, however, be some value in evaluating whether we are at a point, in terms of number of deployment and support models for the same, wherein a Galaxy admin specific group or mailing list would make sense. We have had an estimated six to ten participants at the meet-ups that have occurred since September 2012. Best regards, Srinivas. -Original Message- From: Hans-Rudolf Hotz h...@fmi.ch Date: Monday, April 8, 2013 3:21 AM To: Srinivas Maddhi srinivas-mad...@uiowa.edu, Dave Clements cleme...@galaxyproject.org Cc: Galaxy Dev List galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] GalaxyAdmins Group: Future Directions? Hi Srinivas Thank you very much for e-mail...and thereby reminding me that I haven't replied to Dave's call a week ago. I second most of your thoughts. However, I am not sure of the idea of creating a full-fledged user group with additional opportunities for sharing, learning and collaborating. I like it, but how do you intend to distinguish this group from the current '[galaxy-dev]' group/community? I am afraid stuff will get lost between the two groups or it leads to duplication.probably something we need to discuss in Oslo? I am definitively in favor of a dual leadership - one person from the admin community and one from the Galaxy team. Regards, Hans-Rudolf PS: Do you have stats of who (or how many) has taken part in the past meetups? I think the numbers have been much smaller than the number of responses to Ann's original proposal last April. On 04/05/2013 10:43 PM, Maddhi, Srinivas wrote: Hello, Based on my observations and interactions during the past few meet-ups and as an administrator of Galaxy, the current goals of the group [1] remain relevant and are being met through the meet-ups. An additional benefit to these meet-ups that has evolved is an update from a member of the Galaxy team on upcoming features and other developments. With regard to the future of the group, my suggestion is to keep it going and work towards building a full-fledged user group with additional opportunities for sharing, learning and collaborating. This will strengthen the community, possibly drive increased adoption, and further serve to guide development of Galaxy. Appointing one of more leaders (one each from the Galaxy team and user community) to identify speakers, drive the agenda, set a cadence to the meet-ups and drive the formation of a user group would be helpful, IMHO. Thanks! Notes: 1. Build a community, learn from each other From: Dave Clements cleme...@galaxyproject.org mailto:cleme...@galaxyproject.org Date: Monday, April 1, 2013 11:07 AM To: Galaxy Dev List galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] GalaxyAdmins Group: Future Directions? Hello all, The GalaxyAdmins group is coming up on it's one year anniversary (coinciding with GCC2013) and this is a good opportunity to discuss what the future of the group should be. Some starting topics for discussion are on the GalaxyAdmins Future Directions page (http://wiki.galaxyproject.org/Community/GalaxyAdmins/Future). These include * What should the group's goals and activities be? * What type of leadership structure should the group have, and how should it be selected? The discussion, however, is wide open to any topic relevant to the group. If you have any opinions or suggestions please reply to the group. Anyone with an interest in the group is encouraged to post. Once the discussion settles, I will summarize the discussion on the wiki page and suggest an action plan for making those things happen. Thanks, Dave C. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Dataset generation errors
Hi,
I get this error, what can I do in order to solve this problem?
Traceback (most recent call last):
File
/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/tools/source/upload.py,
line 596, in module
__main__()
File
/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/tools/source/upload.py,
line 566, in __main__
add_file( dataset, registry, json_file, output_path )
File
/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/tools/source/upload.py,
line 217, in add_file
elif check_netcdfwithtimeaxis( dataset.path ):
File
/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/tools/source/upload.py,
line 134, in check_netcdfwithtimeaxis
mod = import_module('earthsystem.NetCDFwithTimeAxis','NetCDFwithTimeAxis')
File
/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/tools/source/upload.py,
line 96, in import_module
fp, pathname, description = imp.find_module(name)
ImportError: No module named earthsystem.NetCDFwithTimeAxis
Thank you,
Ramão
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Re: [galaxy-dev] setup grid engine
Hi Nate, I figured it out. You are right, the same path is required on both the galaxy server and the cluster. I have added the galaxy account on the cluster and point to the same NFS directory. Now it is working for me. Thank you. Jingzhi On Apr 9, 2013, at 9:03 AM, Jingzhi Zhu wrote: Hi Nate, Yes, the directory does exist in the NFS share. I can see galaxy_15.sh exists in this directory, but not the galaxy_15.o and galaxy_15.e file. $ ls -l /net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/ total 129 -rwxrwxr-x 1 love-galaxy love-galaxy 1889 Apr 8 21:15 galaxy_15.sh -rwxrwx--- 1 love-galaxy love-galaxy 2543 Apr 8 21:15 metadata_in_HistoryDatasetAssociation_15_cJgqA4 -rwxrwx--- 1 love-galaxy love-galaxy 20 Apr 8 21:15 metadata_kwds_HistoryDatasetAssociation_15_KHQqa8 -rwxrwx--- 1 love-galaxy love-galaxy0 Apr 8 21:15 metadata_out_HistoryDatasetAssociation_15_CztZ4c -rwxrwx--- 1 love-galaxy love-galaxy2 Apr 8 21:15 metadata_override_HistoryDatasetAssociation_15_3UAQKB -rwxrwx--- 1 love-galaxy love-galaxy 41 Apr 8 21:15 metadata_results_HistoryDatasetAssociation_15_vvt6Jv Thanks, Jingzhi On Apr 9, 2013, at 8:25 AM, Nate Coraor wrote: On Apr 8, 2013, at 9:24 PM, Jingzhi Zhu wrote: Hi Nate, That's it! After I made that change, I was able to see jobs are successfully submitted to the SGE queue and then run. So this is great! I now run into another issue. galaxy.jobs.runners.drmaa DEBUG 2013-04-08 21:16:56,386 (15/530948) state change: job finished, but failed galaxy.jobs.runners ERROR 2013-04-08 21:16:56,526 (15/530948) Job output not returned from cluster: [Errno 2] No such file or directory: '/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o' galaxy.jobs DEBUG 2013-04-08 21:16:56,559 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-04-08 21:16:56,603 setting dataset state to ERROR galaxy.jobs DEBUG 2013-04-08 21:16:56,796 job 15 ended Google search shows a lot of similar errors, but it is never clear how to resolve it. When this job is run, qstat -j shows the following stderr_path_list: NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.e stdout_path_list: NONE:KI-GALAXY:/net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.o script_file: /net/rowley/ifs/data/love/love-galaxy/job_working_directory/000/15/galaxy_15.sh I can see the galaxy_15.sh exists in the above directory, but the galaxy_15.o and galaxy_15.e do not exist during the job run. Where are those files saved? Do you have any idea how to fix it? Thank you so much! Hi Jingzhi, Please use reply all to keep replies on the list. Does that directory exist on the cluster? A shared filesystem mounted at the same path is (currently) required between Galaxy and the cluster. --nate Jingzhi On Apr 8, 2013, at 4:46 PM, Nate Coraor wrote: Hi Jingzhi, Unfortunately, there's a mistake in the sample config for that runner plugin, the line to load the plugin should be: plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ The sample config was fixed in a later commit to the stable branch, and seeing as there was a security release today I would suggest just updating your Galaxy installation to the latest stable commit anyway: % hg pull % hg update stable --nate On Apr 8, 2013, at 4:14 PM, Jingzhi Zhu wrote: I have downloaded the 04_01 release and tried to configure the Sun Grid Engine so that the job can run on our cluster. I have export the DRMAA_LIBRARY_PATH environment variable (export DRMAA_LIBRARY_PATH=/home/love-galaxy/bin/libdrmaa.so.1.0). Then copy job_conf.xml.sample_advanced to job_conf.xml. I have deleted some lines on the plugins section so it looks like this in job_conf.xml 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=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAARunner/ /plugins The run.sh returns the following error galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,465 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2013-04-08 15:57:12,466 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2013-04-08 15:57:12,472 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-04-08 15:57:12,474 Starting job handler galaxy.jobs.runners DEBUG 2013-04-08 15:57:12,475 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-04-08 15:57:12,477 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File /net/rowley/ifs/data/love/love-galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 37, in
[galaxy-dev] problem with BWA
Hello Celso, This problem is occurring in a local install of Galaxy? If so, then you will need to set up the reference genome to be used with tools. Instructions to do so are on these wiki pages: Basic instructions, you will need to move on to Advanced Configuration: http://wiki.galaxyproject.org/Admin/Get%20Galaxy Tool set up (the header is most important for you now, since BWA is already installed): http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Data set up: A version of your genome is available via rsync, with the dbkey Zea_mays_B73_RefGen_v2. Or, you can create your own indexes. The builds.txt list is not optional, so make sure not to skip that part and to restart your server after all steps in the set-up are complete. http://wiki.galaxyproject.org/Admin/Data%20Integration http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Next time, please send questions directly to the mailing list. This will get you the speediest reply. Take care, Jen Galaxy team On 4/8/13 12:11 PM, c cortes wrote: Hello Jen, my name is Celso, i'm trying to map some reads from maize to the reference genome B73 in Galaxy. However when i try with map with BWA for Illumina in the option select a reference genome none file appears neither for use a built-in index nor use one from the history options. I downloaded the B73 file as a fasta file, but my doubt is the way of upload my reference genome in orden to it apperas in Galaxy for mapping Kind regards -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/
