[galaxy-dev] Problem with Torque/Maui
Hi all, first of all, thanks to the Galaxy Team for this really useful software. Actually I don't really know if my problem is related with Galaxy or with Torque/Maui but I didn't find any solution looking in both Torque and Maui user lists, so I hope that some of you with more experience could give me some good advices. I'm trying to set up Galaxy in a small local virtual environment in order to test it. I started with 2 virtual ubuntu servers called galaxy1 and galaxy2. On galaxy1 I succesfully installed Galaxy, Apache, Torque and Maui. I'm using Postgres ad DBMS. It is installed on another real DB server. The virtual server galaxy2 is used as node. Galaxy is working like a charm locally but when I try to use Torque problems arise. Torque alone works correctly. That means that I can submit a job with qsub and everything works. The 2 virtual server (galaxy1 and galaxy2) share a directory (through NFS) in which I installed Galaxy following the unified method from the documentation. Now, as I said, Galaxy alone works, Torque/Maui alone works. When I put the two together nothing works. As a test I upload (using local runner) a gff file. Then I try to make a filter to the gff using Filter and sort - Extract features. When I run this tool the corresponding job on the Torque queue runs forever in Hold state. I report some output from diagnose programs: The diagnose -j reports the following: Name State Par Proc QOS WCLimit R Min User Group Account QueuedTime Network Opsys ArchMem Disk Procs Class Features 29 Hold DEF1 DEF 1:00:00 01 galaxy galaxy-00:02:36 [NONE] [NONE] [NONE]=0=0NC0 [batch:1] [NONE] While the showq command reports ACTIVE JOBS JOBNAMEUSERNAME STATE PROC REMAINING STARTTIME 0 Active Jobs 0 of1 Processors Active (0.00%) IDLE JOBS-- JOBNAMEUSERNAME STATE PROC WCLIMIT QUEUETIME 0 Idle Jobs BLOCKED JOBS JOBNAMEUSERNAME STATE PROC WCLIMIT QUEUETIME 29 galaxy Hold 1 1:00:00 Wed May 4 03:56:40 The checkjob reports: checking job 29 State: Hold Creds: user:galaxy group:galaxy class:batch qos:DEFAULT WallTime: 00:00:00 of 1:00:00 SubmitTime: Wed May 4 03:56:40 (Time Queued Total: 00:03:07 Eligible: 00:00:01) The qstat -f reports Job Id: 33.galaxy1.research.intra.ismaa.it Job_Name = 27_extract_features1_marco.more...@iasma.it Job_Owner = gal...@galaxy1.research.intra.ismaa.it job_state = W queue = batch server = galaxy1.research.intra.ismaa.it ctime = Wed May 4 04:56:36 2011 Error_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.e exec_host = galaxy2/0 exec_port = 15003 Execution_Time = Wed May 4 05:26:41 2011 mtime = Wed May 4 04:56:37 2011 Output_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27. o qtime = Wed May 4 04:56:36 2011 Resource_List.neednodes = 1 Resource_List.nodect = 1 Resource_List.nodes = 1 Resource_List.walltime = 01:00:00 stagein = /mnt/equallogic1/galaxy/tmp/dataset_18.dat@galaxy1 :/mnt/equallog ic1/galaxy/galaxy-dist/database/files/000/dataset_18.dat, /mnt/equallogic1/galaxy/tmp/dataset_30.dat@galaxy1 :/mnt/equallogic1/g alaxy/galaxy-dist/database/files/000/dataset_30.dat stageout = /mnt/equallogic1/galaxy/galaxy-dist/database/files/000/dataset_ 30.dat@galaxy1 :/mnt/equallogic1/galaxy/galaxy-dist/database/files/000/ dataset_30.dat substate = 37 Variable_List = PBS_O_QUEUE=batch, PBS_O_HOST=galaxy1.research.intra.ismaa.it euser = galaxy egroup = galaxy hashname = 33.galaxy1.research.intra.ismaa.it queue_rank = 33 queue_type = E StartDate: -00:03:06 Wed May 4 03:56:41 Total Tasks: 1 Req[0] TaskCount: 1 Partition: DEFAULT Network: [NONE] Memory = 0 Disk = 0 Swap = 0 Opsys: [NONE] Arch: [NONE] Features: [NONE] IWD: [NONE] Executable: [NONE] Bypass: 0 StartCount: 1 PartitionMask: [ALL] PE: 1.00 StartPriority: 1 cannot select job 29 for partition DEFAULT (non-idle state 'Hold') and finally the tracejob reports /var/spool/torque/server_priv/accounting/20110504: Permission denied /var/spool/torque/mom_logs/20110504: No such file or directory /var/spool/torque/sched_logs/20110504: No such file or directory Job: 33.galaxy1.research.intra.ismaa.it 05/04/2011 04:56:36 Senqueuing into batch, state 1 hop 1 05/04/2011 04:56:36 SJob Queued at request of gal...@galaxy1.research.intra.ismaa.it, owner = gal...@galaxy1.research.intra.ismaa.it, job name = 27_extract_features1_marco.more...@iasma.it, queue = batch 05/04/2011 04:56:37 SJob Run at request of gal...@galaxy1.research.intra.ismaa.it 05/04/2011 04:56:41 SEmail 's' to gal...@galaxy1
[galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output
Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html The only problem I had was setting default columns, which I consider to be a minor bug in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/507 Regardless of this small usability issue, would the Galaxy team like to add this tool to the main distribution (to sit along with my BLAST+ wrappers), or should I submit it to the tool shed? If you want to merge it, the following change set should suffice: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 I made a subsequent change set to test giving column defaults as value=c2 rather than value=c2 which makes no difference, but if this is how default column values are meant to be given, take this change too: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 Thanks, Peter ___ 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/
Re: [galaxy-dev] Display BAM with IGV
Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working? Thanks, Dave On 4/27/11 9:07 PM, Dave Walton dave.wal...@jax.org wrote: I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave On 4/27/11 12:33 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Alex, Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see Using a Proxy server at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up. Thanks for using Galaxy, Dan On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote: 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/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam 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/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL 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/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length ___ Alexander Graf Laboratory of Functional Genome Analysis Gene Center, University of Munich (LMU) Feodor-Lynen-Strasse 25; 81377 Munich; Germany email: g...@lmb.uni-muenchen.de Internet: www.lafuga.de/genomics.htm http://www.lafuga.de/genomics.htm ___ ___ 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/ ___ 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/
Re: [galaxy-dev] python2.6?
Yamshchikov, Vladimir wrote: Hello all, If this question is not for this list, please advise. Both my RHEL55 and SL55 are based on python 2.4.3 - how I can add python 2.6 support for Galaxy without screwing up OS? I had both 2.4 and 2.6 installed, by python -V returns only 2.4.3. When I uninstalled 2.4.3, SL55 self-destructed, the same will happen with RHEL55. I was advised that 2.6 should not ever be made seen (like manipulating $PATH) by the system that depends on 2.4 - so how I add 2.6 if it is needed for full functionality? Hi Vladimir, You could install 'python26' from EPEL[1], presumably this does not break /usr/bin/python since it installs the new version as /usr/bin/python2.6. Then as the user which runs Galaxy, do something like this: $ mkdir $HOME/bin $ ln -s /usr/bin/python2.6 $HOME/bin/python $ export PATH=$HOME/bin:$PATH $ echo 'export PATH=$HOME/bin:$PATH' $HOME/.bash_profile --nate [1] http://fedoraproject.org/wiki/EPEL ___ 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/ ___ 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/
[galaxy-dev] Restoring galaxy database return few empty tables.
Dear Galaxy Team, I am switching our Galaxy production service to a new machine, We are using Postgres as database server. The existing database belongs to postgres version 8.3 and I took my instance's dump using postgres version 8.4. I am able to restore my database on postgres 8.4, Except few tables were empty and with few strange error message left on log file. I am not sure how many tables are empty, but I found table called 'job' returns 0 rows. Original job table returns me 40733 rows. excerpts from error log: ERROR: insert or update on table history_dataset_association_annotation_association violates foreign key constraint history_dataset_association_a_history_dataset_association__fkey DETAIL: Key (history_dataset_association_id)=(284985) is not present in table history_dataset_association. STATEMENT: ALTER TABLE ONLY history_dataset_association_annotation_association ADD CONSTRAINT history_dataset_association_a_history_dataset_association__fkey FOREIGN KEY (history_dataset_association_id) REFERENCES history_dataset_association(id); ERROR: insert or update on table history_dataset_association_tag_association violates foreign key constraint history_dataset_association_t_history_dataset_association__fkey DETAIL: Key (history_dataset_association_id)=(387932) is not present in table history_dataset_association. STATEMENT: ALTER TABLE ONLY history_dataset_association_tag_association In my knowledge we didn't do any manual transactions on Galaxy database and Could anyone let me know something wrong at my end. I'm sure this has been covered somewhere but I haven't been able to find it on the Wiki or by searching the archives. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany ___ 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/
