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

bug or feature :)
by Bossers, Alex 31 Aug '11

31 Aug '11

In our local instance (central version) up to changeset (June 28th) I noticed in the admin panel to manage jobs some odd behaviour; When I set the update Jobs cutoff on 10 seconds and press refresh.... the item below (administrative Job Lock) is also activated and new jobs are locked. Is that a planned feature, a bug or is something wrong in our local instance. Another refresh toggles it back to normal. Alex

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Wrapper generator.
by J. F. J. Laros 31 Aug '11

31 Aug '11

Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - J.F.J.Laros(a)lumc.nl

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[API] Error message forwarding
by Louise-Amélie Schmitt 29 Aug '11

29 Aug '11

Hi, I ran into a little something that is a bit annoying for debug when trying to upload files through the API with library_upload_from_import_dir.py. When the specified folder is wrong, python tries to process the error tuple like a dict, so the original error is hard to find. I modified a little the code to avoid that. It might not work in all cases but at least it solved my problem. Here is the original code: lib/galaxy/web/api/contents.py l.145->end else: rval = [] for k, v in output.items(): if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) return rval Here is how I modified it: else: rval = [] try: for k, v in output.items(): if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) return rval except: log.debug( 'HTTP Error %s: %s' % ( output[0], output[1] ) ) return None Since it saves me some time & energy I just wanted to share it, so I hope it can help. Best L-A

2 1

Updated Cufflinks Wrapper
by Chorny, Ilya 25 Aug '11

25 Aug '11

I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still be updated in my commit. https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5 Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Error when using build_profile_indexes.py on hg19
by Sarah Diehl 25 Aug '11

25 Aug '11

Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). ['fileName'] Table wgEncodeOpenChromFaireGlioblaBaseOverlapSignal (/galaxy/galaxy_data/ucsc_data/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop. Removing empty table (wgEncodeOpenChromFaireGlioblaBaseOverlapSignal) directory (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). Created table dir (profiled_annotations/hg19/wgEncodeCshlShortRnaSeqK562ChromatinShortTransfrags). ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand', 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount', 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount', 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount', 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength', 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY'] Traceback (most recent call last): File "/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py", line 338, in <module> if __name__ == "__main__": __main__() File "/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py", line 310, in __main__ bitset_dict[ chrom ].set_range( start, end - start ) File "bitset.pyx", line 128, in bx.bitset.BitSet.set_range (lib/bx/bitset.c:1130) File "bitset.pyx", line 93, in bx.bitset.b_check_range_count (lib/bx/bitset.c:656) IndexError: End 16573 is larger than the size of this BitSet (16571). Everything worked fine with mm9 and dm3. Since the script wasn't changed in the last year, I suspect it has to do with the UCSC data. We don't really use hg19, so I'm fine with just leaving it out for now, but I wanted to report the error anyway. Best regards, Sarah

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checkboxes bug fix
by Louise-Amélie Schmitt 25 Aug '11

25 Aug '11

Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ for: 105 return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="false"%s>' \ And it works fine now :) Cheers, L-A

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Launching a JAVA or external app
by Bossers, Alex 24 Aug '11

24 Aug '11

Hello all, would it be possible to launch for instance a JAVA app with preloaded parameters and files from galaxy that needs interaction/display? For instance a gui based annotation editor? It necessarily doesn't have to support saving of files back to galaxy. Sort of end stage. Any help or pointers appreciated. thanks Alex

2 1

collect_associated_files and umask
by Chorny, Ilya 23 Aug '11

23 Aug '11

When I run galaxy as the actual user using the code I committed to my fork, I run into a problem with dataset_*.dat files that have associated data wherein the associated data files are copied from the job_working_directory into the files directory. That directory is owned by the actual user and not by the galaxy user. I don't have a problem with the ownership but the permissions of the directory and associated files get changed to 777. Any thoughts on why the permissions get changed. The permissions are 755 and 644 for dirs and files respectively when in the working directory so why do they change when the directory is moved? Any help would be greatly appreciated. Best, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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problem with build_chrom_db.py
by Curt Palm 22 Aug '11

22 Aug '11

I've been configuring my local instance of galaxy to use trackster according to the instructions on https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization when I run the script: python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ I get files that begin with: <META http-equiv="Content-Script-Type" content="text/javascript"> chr1 247249719 chr1_random 166326 ... this causes an error in the browser: "Could not load chroms for this dbkey:" if i delete the first line " <META http-equiv="Content-Script-Type" content="text/javascript">" from the .len file, then trackster works fine. I'm thinking there is a new line the input to build_chrom_db.py that is not getting stripped by this script thanks, Curt Palm ******************************************************* Curtis J. Palm cpalm(a)stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994 cell: 408 858-7849 *******************************************************

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upload.py fails with files having commas in file name
by Chorny, Ilya 22 Aug '11

22 Aug '11

The ftp upload module fails when a file has a comma in the file name for example test.bam works but when copied to test,test.bam that file fails. Cheers, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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