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problem running latest "galaxy-central"
by Assaf Gordon 29 Apr '11

29 Apr '11

Question: The recent galaxy-central revision ( 2b057869b72f ) doesn't work on my computer, saying "DistributionNotFound: cython>=0.12.1". Example: $ hg clone http://bitbucket.org/galaxy/galaxy-central/ galaxy_hidden_dataset_test $ cd galaxy_hidden_dataset_test $ hg id 2b057869b72f tip $ sh run.sh ... ... ... Traceback (most recent call last): File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/visualization/tracks/data_providers.py", line 11, in <module> pkg_resources.require( "pysam" ) File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 404, in require return c[req.project_name].require() File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 237, in require dists = self.resolve() File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here DistributionNotFound: cython>=0.12.1 ============= I'm running debian/stable, with Python 2.6.6 (r266:84292, Dec 26 2010, 22:31:48) Do I need to install something (cython) ? -gordon

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Data libraries management: error on moving a dataset
by Joachim Jacob 29 Apr '11

29 Apr '11

Hi all, I just upgraded my version of Galaxy to the latest one. No probs with that. But in "Manage Data Libraries", the 'move this dataset' option however seems to give an error on our installation: *Not Found The resource could not be found. No action for /library_common/move_library_item* Does anyone else has this error? Cheers, Joachim -- Joachim Jacob. ------------------------------------------------------------------------ BITS logo <http://www.bits.vib.be/training> Joachim Jacob, PhD. <http://be.linkedin.com/in/joachimjacob> Bioinformatics Trainer BITS - www.bits.vib.be <http://www.bits.vib.be/> VIB - www.vib.be <http://www.vib.be/> BITSrssFeed <http://www.bits.vib.be/index.php?option=com_ninjarsssyndicator&feed_id=3&fo…> Skype Me^(TM)! <skype:joachim.at.bits?call> Follow bitsatvib on Twitter <http://www.twitter.com/bitsatvib> VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium (see map <http://maps.google.be/maps/ms?ie=UTF8&hl=nl&msa=0&msid=11098443444793876801…>) | Tel.: +32 9 244 66 34 | Fax.: +32 9 244 66 10

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anyone actually properly implemented remote_user_logout_href with external HTTP authentication?
by Leandro Hermida 29 Apr '11

29 Apr '11

Hi everyone, Has anyone actually properly implemented remote_user_logout_href in Galaxy with external HTTP authentication? As probably those who have tried know, it is rife there doesn't seem to be a clean and robust way to do this? best, Leandro

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User Name "not set" with external LDAP authentication
by Leandro Hermida 29 Apr '11

29 Apr '11

Hi, Just wondering if I got my setup right, I have Galaxy front-ended by Apache doing the static caching, proxying and LDAP auth. What's nice is that user's don't have to be created by an admin if the user authenticates and authorizes properly against the LDAP config then Galaxy will automatically create the user locally. My question is that it shows that the User Name is "not set" for such users, is this the way its supposed to be or can I modify my LDAP config in such a way that it does set a User Name? regards, Leandro

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Getting tool dirpath in a Python code file
by Leandro Hermida 29 Apr '11

29 Apr '11

Hi, I have a tool with a <code file="my_script.py"/> tag and in that code file I'm trying to get the tool dirpath where that script and the tool XML exist. I've tried: os.path.abspath(os.path.dirname(sys.argv[0])) os.path.abspath(os.path.dirname(__file__)) And both don't work as expected. Is there a galaxy class I could import which will have the tool directory path? regards, Leandro

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Huge Output Files in Galaxy (in compute cluster)
by Marc Bras 29 Apr '11

29 Apr '11

Hi All, I use Galaxy on a compute cluster and each job is launch in a node. When I launch a workflow and when it generates very huge files (some Go), the job finish (I can see that with 'qstat' command) but Galaxy takes several minutes (or some hours !!) to display a green Box in history. It seems running... but it's already finished in the cluster !! I think Galaxy is checking the output file... Is it normal ? Is it possible to skip this check ? Thanks in advance, Marc -- Marc Bras ------------------------------------------ Marc.Bras(a)versailles.inra.fr INRA-URGI: Unité de Recherche Génomique Info Centre de Recherche de Versailles-Grignon Route de Saint Cyr 78026 Versailles - FRANCE Tel: +33 1 30 83 34 70 ------------------------------------------

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Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
by Whyte, Jeffrey 28 Apr '11

28 Apr '11

Hi Everyone, I'm having trouble getting some of the tools to work on my local installation of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy wiki are clear, and I was able to download and install from the anonymous Mercurial repository. Galaxy starts up and runs just fine for tools like "Get Data", "FASTQ Groomer", and "FASTQ Summary Statistics". The problems started when I try to run Graph/Data Display -> Boxplot (GnuPlot). I get the error: "An error occurred running this job:/bin/sh: gnuplot: command not found Error running gnuplot." The FASTX Barcode Splitter also gives me an error: "An error occurred running this job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file or directory sed: illegal opt" I'm assuming these are Tool Dependency problems, although I have tried to install the OS X versions of GnuPlot and the FASTX Toolkit and still get errors. Are there any suggestions from users who are successfully running Galaxy on OS X? Thanks in advance, Jeff

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Launching multiple jobs using one tool form with multiple selected datasets
by Leandro Hermida 28 Apr '11

28 Apr '11

Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro

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Does REMOTE_USER have to be an email address?
by Leandro Hermida 27 Apr '11

27 Apr '11

Hello, When returning REMOTE_USER env var from the external authentication method does it have to be an email address for Galaxy? The docs aren't very clear on that, in the main External Authentication section it says you have to have to set remote_user_maildomain if you aren't return an email address (and the domain will be appended it seems) but in the mod_authnz_ldap section it says you are allowed to set any attribute to return as REMOTE_USER. regards, Leandro

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Question on finding external_filename and _extra_files_path from psql DB.
by Vipin TS 26 Apr '11

26 Apr '11

Dear Galaxy Team, As a part of in-house automated cleaning of data set from our production galaxy service, I am finding difficulty to get the galaxy assigned file name (galaxy-root/database/001/dataset_001.dat) for each data set from the corresponding database. We are using PostgreSQL and when I queried through the table name called 'dataset', couldn't figure out the values for external_filename or _extra_files_path. For example: >> select * from dataset order by id DESC limit 10; id | create_time | update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size 70805 | 2011-04-22 20:49:55.319709 | 2011-04-22 20:50:26.643807 | ok | f | f | t | | | 421593 Could you please let me know where I can locate the file name from other tables or do I need to set up any configuration. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany

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