April 2011 - galaxy-dev - lists.galaxyproject.org

Question Regarding Local Galaxy Installation Uploading Files Error
by George Yianni Michopoulos 02 May '11

02 May '11

To any wonderful person that can help me: I recently uploaded a local instance of Galaxy on a new computer at the Fernald Lab at Stanford. I am not too familiar with Unix, but needed to install the local instance due to the high volume of genomic data we will be processing, and so that we could install/use the FastX toolkit. I managed to successfully install the toolkit, but now I just realized that I can't seem to upload any of my correctly formatted data files. The error I get is pasted below: "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.18.1 (KHTML, like Gecko) Version/5.0.2 Safari/533.18.5" Debug at: http://localhost:8080/_debug/view/1303859435 ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 61553) Traceback (most recent call last): File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__ return app(environ, start_response) File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params params = self.str_params File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 892, in str_params return NestedMultiDict(self.str_GET, self.str_POST) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST keep_blank_values=True) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__ self.read_single() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single self.read_lines() File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/base.py", line 253, in read_lines self.read_lines_to_outerboundary() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary line = self.fp.readline(1<<16) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 467, in readline data = self.file.readline(self.length - self._consumed) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline bline = buf.readline(size) OverflowError: long int too large to convert to int" (I replaced irrelevant components of the file path with *** for confidentiality purposes) Do you have any idea what the problem is and how I can fix it? I feel like it has something to do with my python, but I downloaded 2.6.6, which I thought should work according to the Install Readme. Thanks so much for your help! Sincerely, George Michopoulos Stanford University '13 on behalf of the Fernald Lab

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tool parameter attribute for option display value (not passed value)?
by Leandro Hermida 02 May '11

02 May '11

Hi, For a tool select input parameter: <param name="input1" type="select"> <option value="hs33">Homo sapiens</option> <option value="mm19">Mus musculus</option> <option value="rn43">Rattus norvegicus</option> </param> Is there an attribute for the variable $input1 that will give me the displayed value (e.g. Homo sapiens, not hs33)? thank you, Leandro

2 1

Link address to specific section of tools in Galaxy
by Vipin TS 29 Apr '11

29 Apr '11

Dear Galaxy Team, Any idea how I can access a specific section of tools from a Galaxy instance ? For example: In our Galaxy instance at http://galaxy.tuebingen.mpg.de/, we have a section called 'Gene Finding'. Under this we have several sub sections and I would like to invoke a specific sub section let's say mGene.web through a link address. In Galaxy I know we can specifically call a tool page through the link address. My concern is that if I call for the sub section, is there any chance to load the first tool from that section to the tool page and list the available tools in tool panel frame. Many thanks for your great effort. Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany

2 1

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

2 4

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

2 3

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

3 6

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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