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

Galaxy Community Conference Registration Closes May 17
by Dave Clements 09 May '11

09 May '11

Hello all, We are closing registrations for the Galaxy Community Conference at the end of May 17. However, the conference is likely to fill up before that date. So, if you are thinking about attending, *now* is the time to register for the meeting: http://galaxy.psu.edu/gcc2011/Register.html We have also secured some additional rooms on the night of May 24, in a hotel in Lunteren: http://galaxy.psu.edu/gcc2011/Logistics.html Again, it is not necessary to stay in Lunteren the night of May 24, as it is easy to get there from Amsterdam on May 25, before the meeting starts. Finally, a draft schedule is now available at: http://galaxy.psu.edu/gcc2011/Programme.html This is still subject to change, but we are hoping it won't change much. Just 15 days to go! Dave C. -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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problems previewing certain files, downloading files and with login
by Matthew Conte 09 May '11

09 May '11

Good afternoon, I'm having several problems with my local galaxy install which may or may not be related to one another. The first problem I'm having is with the "Display data in browser" feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the "Display data in browser" eyeball icon. It is simply a blank middle panel. The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download: *This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the connection.* In this case, I don't see anything in the log files either. Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page. For this problem, I do get an error in the galaxy log: *Exception happened during processing of request from---------------------------------------- * *('myip', 50593)Exception happened during processing of request from * *('myip', 50594)* *Traceback (most recent call last):* *Traceback (most recent call last):* * File "/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread* * File "/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread* * self.finish_request(request, client_address)* * self.finish_request(request, client_address)* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in finish_request* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in finish_request* * self.RequestHandlerClass(request, client_address, self)* * self.RequestHandlerClass(request, client_address, self)* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in __init__* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in __init__* * self.finish()* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in finish* * self.finish()* * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in finish* *error: [Errno 32] Broken pipe* *----------------------------------------* * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe* I am able to log in via other routes, such as going to "Options->Saved Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScali… Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte(a)umd.edu

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quick question: how can i supply the user's email address to a tool?
by Edward Kirton 09 May '11

09 May '11

is there a variable i can use in the tool config xml file? thanks! ed

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Can I run workflow on certain nodes of the cluster?
by Liisa Koski 09 May '11

09 May '11

Is it possible to run a specific workflow only on certain nodes of the cluster? Either using the API or by setting something in the config files? Thanks, Liisa

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Display BAM with IGV
by Alexander Graf 09 May '11

09 May '11

Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance Alex INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… content-length ___________________________________________________________ Alexander Graf Laboratory of Functional Genome Analysis Gene Center, University of Munich (LMU) Feodor-Lynen-Strasse 25; 81377 Munich; Germany email: graf(a)lmb.uni-muenchen.de Internet: www.lafuga.de/genomics.htm ___________________________________________________________

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Dynamically Specifying PBS Resources
by Allen, Benjamin S 09 May '11

09 May '11

I'm wondering if its possible to somehow present the user with a param that lets him or her specify number of cores, nodes, memory, and wall time from within the workflow for a specific tool. Other than coming up with a predictive algorithm for each tool's resource needs (memory especially) how is one supposed to efficiently use Galaxy and PBS other than somehow letting the user specify needed resources? Think in cases like assembly, for example with Velvet depending on the input files, resource requirements can be vastly different job to job. Thanks, Ben

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shared TEMP directory location
by Shantanu Pavgi 09 May '11

09 May '11

I am configuring galaxy to use a shared filesystem location as it's TEMP directory. I have modified $TEMP variable with the necessary path. Are there any other changes that I need to make? The cluster config page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions about removing or commenting out tool runner configuration, example below: {{{ [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// }}} Should we replace it with some other value or completely remove it? Also, what should it be set to for any additional tools that we install? -- Thanks, Shantanu.

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Unable to set metadata in API call
by Duddy, John 09 May '11

09 May '11

I need to be able to set some metadata in some custom data types. For now, I'm just trying to set the value of the 'misc_info' field. The client script is this: put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' : 'meta data msg' } ) and my API method is as follows. It executes fine, but the values do not show on the next show() call. Disclaimer: Python is still quite new to me, and it's very likely I do not understand the metadata model and the way library dataset associates work. Any clues will be greatly appreaciated! @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id} Sets attributes (metadata) on a library item. """ update_type = None if 'update_type' not in payload: trans.response.status = 400 return "Missing required 'update_type' parameter. Please consult the API documentation for help." else: update_type = payload.pop( 'update_type' ) if update_type not in ( 'metadata' ): trans.response.status = 400 return "Invalid value for 'update_type' parameter ( %s ) specified. Please consult the API documentation for help." % update_type content_id = id decoded_type_and_id = trans.security.decode_string_id( content_id ) content_type, decoded_content_id = decoded_type_and_id.split( '.' ) if content_type not in ( 'file' ): trans.response.status = 400 return "Updates allowed only on files, not directories" try: content = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( decoded_content_id ) except: content = None if not content or ( not trans.user_is_admin() and not trans.app.security_agent.can_modify_library_item( trans.get_current_user_roles(), content, trans.user ) ): trans.response.status = 400 return "Invalid %s id ( %s ) specified." % ( content_type, str( content_id ) ) metadata = content.get_metadata() content.datatype.before_setting_metadata(content) if not metadata: metadata = {} for name in payload: if name not in [ 'name', 'info', 'dbkey' ]: setattr( metadata, name, payload[name]) content.set_metadata(metadata) content.datatype.after_setting_metadata( content ) trans.sa_session.flush() return "OK" John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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Concatenation as first step in workflow
by Dave Walton 09 May '11

09 May '11

We have samples that span multiple lanes of our sequencer, that are the same sample. We'd like to have workflows where the first step is to concatenation the fastq files for one sample, and then feed it to the rest of our workflow (for RNA Seq). Unfortunately, when I use the Concatenation module as the first step in my worflow, it doesn't have the "Add New Dataset" button appear when running the workflow, and I don't see a way to force it in the workflow editor to "Set at runtime". Is this a bug? Is there a fix forthcoming? Sure I could do this concatenation as a stand-alone module first and then run the workflow separately with my new fastq file, but for my users I'd rather it be part of the workflow. Thanks, Dave

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Wrappers for NCBI BLAST+ blastdbcmd
by Peter Cock 09 May '11

09 May '11

Hi all, I've done a couple of wrappers for the NCBI BLAST+ tool blastdbcmd. The NCBI BLAST+ tool blastdbcmd replaces the NCBI legacy BLAST tool fastacmd. The wrapper first lets you get a FASTA file of sequences from a database by their ID (which works best if your database was built with -parse_seqids), while the second just shows a information about a database like number of sequences and total length (human readable text). Branch here: https://bitbucket.org/peterjc/galaxy-central/src/blastdbcmd Two files: tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Is anyone interested in helping to test these before I ask the Galaxy team to merge them into the trunk? Those of you familiar with the command line tool's options will know you can use -entry all to get all the sequences in the database. This is fine for a small database (e.g. a single genome), but would be a really bad idea for something like the NCBI NR database. Currently there is no safety check for this (but it could be done with a wrapper script that asks via the -info switch how many sequences there are). Do you think some defensive code is a good idea here, e.g. a limit of 5000 sequences when "all" is used? Thanks, Peter

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