April 2013 - galaxy-dev - lists.galaxyproject.org

"Local install" of Galaxy Tool
by Holtgrewe, Manuel 11 Apr '13

11 Apr '13

Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows: <command>BINARY (arguments)</command> When I put the following, it works: <command>$__root_dir__/tools/CATEGORY/BINARY</command> Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try? Thanks! Manuel [1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial

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adding datatypes in tool xml
by Robert Baertsch 10 Apr '13

10 Apr '13

If I want to add a new datatype during tool installation from the shed, how define that in the tool.xml? Is this documented anywhere? -Robert

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How can I creating a tool in C++
by Ramon Tiburski 10 Apr '13

10 Apr '13

Hi,I need to create a new tool in c++, but I'm with a lot of difficult to link the cpp or exe (I don't know) with the xml document. Can you help me with an example that receives a txt file with a phrase and shows another txt file without the spaces of this phrase? Thanks

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Why Galaxy? What the advantages?
by Ramon Tiburski 10 Apr '13

10 Apr '13

I started studying the galaxy and would like to know about the power of this tool, you could tell me why using the galaxy and what are its advantages compared to other similar systems. And another question, can I adapt galaxy to another area like the agronomy, only with creating new tools? Thanks

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Bowtie2 and Tophat2 versions
by Lance Parsons 10 Apr '13

10 Apr '13

I noticed that the latest versions for Bowtie2 and Tophat2 listed on the Tool Dependencies page (http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies) are 2.0.4 for Bowtie2 and 2.0.6 for Tophat2. Are these the latest supported versions? Does anyone know if it's advisable to go with the latest (Bowtie2 2.1.0 and Tophat 2.0.8) with Galaxy? I'm looking forward to these tools being moved to the ToolShed so updates to the underlying tools are accompanied by Galaxy tool version updates, but until then I'm just trying to make sure my users can use the latest versions that are compatible. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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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 09 Apr '13

09 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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