June 2010 - galaxy-dev - lists.galaxyproject.org

import error: no file bz2
by wenqing zhang 22 Jun '10

22 Jun '10

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Re: [galaxy-dev] Installing galaxy with sge
by Nate Coraor 22 Jun '10

22 Jun '10

Originally posted on galaxy-user: Mariette wrote: > Hi everyone, > I installed galaxy on our system and it worked just fine until I tryed > to settled it > up to make it run on our cluster. So I edited the universe_wsgi.ini file > as following: > > # Comma-separated list of job runners to start. local is always > started. If > # left commented, no jobs will be run on the cluster, even if a cluster > URL is > # explicitly defined in the [galaxy:tool_runners] section below. The > runners > # currently available are 'pbs' and 'sge'. > start_job_runners = sge > > # The URL for the default runner to use when a tool doesn't explicity > define a > # runner below. For help on the cluster URL format, see the > ClusteringGalaxy > # Wiki. Leave commented if not using a cluster job runner. > default_cluster_job_runner = sge://INRA_CLC/wflowq//-R y -l h_vmem=8G -l > mem=8G > > I also did the egg thing like this : > > SGE_ROOT=/SGE/n1ge62 python2.5 scripts/scramble.py DRMAA_python > > This line looks like it worked out. > > Then when starting the engine, I'm catching this error : > > Traceback (most recent call last): > File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/web/buildapp.py", > line 61, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/app.py", line 69, in > __init__ > self.job_manager = jobs.JobManager( self ) > File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/__init__.py", > line 40, in __init__ > self.dispatcher = DefaultJobDispatcher( app ) > File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/__init__.py", > line 777, in __init__ > self.job_runners[runner_name] = runners.sge.SGEJobRunner( app ) > File > "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/runners/sge.py", > line 83, in __init__ > self.ds.init( self.default_cell ) > File "build/bdist.linux-x86_64/egg/DRMAA.py", line 186, in init > errParse(eno, estr) > File "build/bdist.linux-x86_64/egg/DRMAA.py", line 167, in errParse > else: raise _errindex[errno-_errMin](errstring) > InvalidArgumentError: The input value for an argument is invalid. > Exception DRMAA.NoActiveSessionError: NoActiveSessionError('',) in > <bound method Session.__del__ of <DRMAA.Session object at 0x104e2bd0>> > ignored > > I'm guessing someting weird is happening with the DRMAA eggs, so I > edited the > /usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/runners/sge.py to > figure out if the module is > well loaded and sounds like it is ! So I'm kind of lost ... do you have > any idea on what is > going on ? Hi Jerome, Did you get any further with this issue? The egg is definitely loading, but this error is very strange - essentially, the library is complaining that there's no active session when we try to create a new session, which is what we want. --nate > > One other weird think is that I had to unset some tools from the > tool_conf.xml when starting > with the sge parameters, what hadn't to be done whitout sge, does it > sounds normal to you ? > > thanks, > Jerome > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Allow zip file upload
by Pablo Cingolani 21 Jun '10

21 Jun '10

Here is a small patch to allow zip file uploads (just one file per zip). See Issue 280 http://bitbucket.org/galaxy/galaxy-central/issue/280/allow-zip-file-uploads I'm new to Galaxy and Python, so I hope I didn't break up anything in the process :-) Find attached a diff file, which I created by executing: hg diff tools/data_source/upload.py > upload.py.diff Please let me know if you prefer another format. Yours P.

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Slow FASTQ-Groomer / Illumina input for tools
by Assaf Gordon 20 Jun '10

20 Jun '10

Hello, We've processing several FASTQ files (Illumina, of course ;) ), and the FASTQ-Groomer is running for 2.5 hours now. The input files are ~4.5GB / 36nt . First, Is any one else getting faster results ? maybe we're doing something wrong that can be improved. Second, Is any one on the mailing-list have Illumina-capable versions of TopHat/Cufflinks, ones that don't require grooming ? Thanks, -gordon

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Composite Datatypes
by Filip Balejko 19 Jun '10

19 Jun '10

Hi, I'm working on the project for Google Summer of Code: https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code… It was going smooth but today I've got stuck and I would really appreciate your help. I'm trying to create a Composite Datatype according to: http://bitbucket.org/galaxy/galaxy-central/wiki/CompositeDatatypes Currently I'm passing $output.files_path to my .py script and then I'm creating my "component" files in this directory. As I've understood from documentation, generate_primary_file method is where I should generate my "primary" output. But It seems that my composite datatype object isn't created - I'm logging some debug in __init__ and generate_primary_file but nothing shows up. Of course I've added this datatype to datatypes_conf.xml. Have I misunderstood something? Should I do something else to get it working? I've looked into: lib/galaxy/datatypes/genetics.py tools/rgenetics/rgfakePed.xml tools/rgenetics/rgfakePed.py and it seems to me that this tool creates its "primary" output in rgfakePed.py (doImport function) and I can't figure out when generate_primary_file method (genetics.py: Rgenetics()) is being called. Thanks, Filip Balejko

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Workflow - Conditional change in output not recognized
by Dennis Gascoigne 18 Jun '10

18 Jun '10

Hi; When a tool has conditional changes in output format, the workflow designer does not recognise the conditional output types. i.e. if the standard output is tabular, but one of the tools settings changes it to interval, you cannot then connect the oiutput node to a tool requiring an interval data type. The workflow designer still treats the other tools output as tabular, even though it should now be interval Is this something that is easily fixed? Cheers Dennis --

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the display of bam files from galaxy behind apache is not working
by TRBarrette 18 Jun '10

18 Jun '10

Hi, I can't see the data at ucsc when I upload a bam file and try to display it. The track arrives at ucsc. I see GET /display_application/... and 200 and bytes in the httpd/access_log I see GET /display_application/... in the paster.log But I don't see the seq reads at the ucsc browser. Some background information: I am setting up our local galaxy server. The server is redhat 5. The IP is external and whether firewall is up or down is immaterial in the behavior. The galaxy install is running at localhost:8080. There is the default redhat apache running in front of galaxy with the rewrite rules enabled for static and all traffic to port 80. Apache security is not enabled (yet). The dedicated galaxy user and group is running galaxy. Thanks, Terry

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Workflow improvement suggestion
by Dennis Gascoigne 18 Jun '10

18 Jun '10

We are finding galaxy really useful but with the implications of users not cleaning up after themselves when running long workflow is hitting on our storage. This could be easily fixed by allowing users to mark steps in a workflow as "KEPT" or "DELETED". Then whenever the workflow is run the files that are just created in passing to the next step and aren't required as output can be automatically marked as deleted and cleaned up as part of normal cleanup operations. Would you consider implementing this, or if not - which modules would be best to look at if we want to do it ourselves? Cheers Dennis

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Viewport generation error
by SHAUN WEBB 18 Jun '10

18 Jun '10

Hi, I am finding the following statements in my paster.log: galaxy.datatypes.interval ERROR 2010-06-18 13:15:42,349 Viewport generation error -> invalid literal for int() with base 10: 'Start' The full traceback is below. This has only started happening in the last few days during which I have updated my Galaxy install and created a new datatype in tabular.py by adding the following code: qclass IndexFile( Tabular ): file_ext = 'indexfile' def sniff( self, filename ): return False and: <datatype extension="indexfile" type="galaxy.datatypes.tabular:IndexFile" display_in_upload="true"/> to datatypes_conf.xml I'm not sure if these are related at all but if anyone could give me a more specific idea about what causes such an error then I would be grateful. Thanks Shaun Webb paste.httpserver.ThreadPool WARNING 2010-06-18 13:14:21,972 Thread 1159838032 hung (working on task for 1914 seconds) paste.httpserver.ThreadPool INFO 2010-06-18 13:14:22,049 Killing thread 1159838032 paste.httpserver.ThreadPool INFO 2010-06-18 13:14:22,112 kill_hung_threads status: 10 threads (4 working, 6 idle, 0 starting) ave time 1098.24sec, max time 1914.39sec, killed 1 workers galaxy.datatypes.interval ERROR 2010-06-18 13:14:30,889 Viewport generation error -> invalid literal for int() with base 10: 'Start' galaxy.datatypes.interval ERROR 2010-06-18 13:14:30,930 Viewport generation error -> invalid literal for int() with base 10: 'Start' 77.99.111.226 - - [18/Jun/2010:13:04:43 +0100] "GET /history HTTP/1.1" 200 - "http://bifx3.bio.ed.ac.uk:8080/history/list?f-deleted=False&f-sharing=All&f…" "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-GB; rv:1.9.0.19) Gecko/2010031422 Firefox/3.0.19 (.NET CLR 3.5.30729)" galaxy.datatypes.interval ERROR 2010-06-18 13:15:36,375 Viewport generation error -> invalid literal for int() with base 10: 'Start' galaxy.datatypes.interval ERROR 2010-06-18 13:15:36,429 Viewport generation error -> invalid literal for int() with base 10: 'Start' ---------------------------------------- Exception happened during processing of request from ('77.99.111.226', 3946) Traceback (most recent call last): File "/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpserver.py", line 1053, in process_request_in_thread galaxy.datatypes.interval ERROR 2010-06-18 13:15:36,758 Viewport generation error -> invalid literal for int() with base 10: 'Start' galaxy.datatypes.interval ERROR 2010-06-18 13:15:36,877 Viewport generation error -> invalid literal for int() with base 10: 'Start' self.finish_request(request, client_address) File "/usr/lib/python2.5/SocketServer.py", line 254, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.5/SocketServer.py", line 523, in __init__ self.finish() File "/usr/lib/python2.5/SocketServer.py", line 568, in finish self.rfile.close() File "/usr/lib/python2.5/socket.py", line 232, in close self.flush() File "/usr/lib/python2.5/socket.py", line 245, in flush def flush(self): SystemExit ---------------------------------------- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Developing Tools With Java
by Elie Freilich 18 Jun '10

18 Jun '10

Hello, I just started working with developing a tool for Galaxy; I have been programming it in Java. However, when it came time to implement my tool into Galaxy, I was unable. When I try to run it normally, it works. However, in Galaxy, when I try to use the JAR file, it produces a java.lang.NoClassDefFoundError and a java.lang.ClassNotFoundException. As it seems rather meaningless to be setting a classpath in an abstract framework like Galaxy, is there a simple way to run Java JAR files? I tried a "-jar" argument, but I can't put in an argument before the filename. Should I be using the ".class" files instead of the JAR files? Should the format in the XML file be <command interpreter="java"></command>? Thanks so much, Elie

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