- galaxy-dev - lists.galaxyproject.org

resubmit a job if the node fails
by zhengqiu cai 10 Apr '13

10 Apr '13

Hi, Can Galaxy resubmit a job if the node where the job is running fails? I know sge can do that by using qsub -r. It should be very useful if Galaxy can do that. Thank you, Cai

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How to be an admin?
by Tobias Hohenaur 10 Apr '13

10 Apr '13

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

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problem with BWA
by Jennifer Jackson 10 Apr '13

10 Apr '13

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

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Re: [galaxy-dev] setup grid engine
by Nate Coraor 09 Apr '13

09 Apr '13

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"> >>>  >>> <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 you show me what the file job_conf.xml should look like? There are a lot of tags in this new XML file and I found it is hard to do it right. >>> >>> Thanks! >>> >>> Jingzhi >>> >>> ___________________________________________________________ >>> 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/ >> >

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Dataset generation errors
by Ramon Tiburski 09 Apr '13

09 Apr '13

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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galaxy local installation
by Yinan Wan 09 Apr '13

09 Apr '13

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. Thanks, Yinan -- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University

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How to test DRMAA configuration?
by Joshua Orvis 09 Apr '13

09 Apr '13

I have a working local Galaxy instance and wanted to enable DRMAA support to utilize our SGE (or LSF) grid. Following the guide here<http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster> 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

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Custom tool need a directory as input
by David Angot 09 Apr '13

09 Apr '13

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

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How to distribute our local installation via git(logistics)
by Perez, Ricardo 09 Apr '13

09 Apr '13

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

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GCC2013 Talk Abstract Submission closes this Friday
by Dave Clements 09 Apr '13

09 Apr '13

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 BGI<http://www.genomics.cn/en/index>will generously cover the article processing fees for these articles. See the announcement <http://wiki.galaxyproject.org/News/GigaScienceGalaxyCFP>for details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://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 Day<http://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 registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://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 submission<http://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 Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > <http://galaxyproject.org/wiki/GCC2012>http://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/

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