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

Galaxy megablastdb indexer script proposal
by Jacob Israel Cervantes Luevano (LANGEBIO) 06 Sep '11

06 Sep '11

Hi Galaxy Dev, Nice to meet you. My name is Jacob and I am from México , Actually I'm working in LANGEBIO (Laboratorio Nacional de Genomica para la Biodiversidad) at Bioinformatics. I would like to contribute with galaxy dev team, I developed shell script to set up reference genomes by megablast. the linux shell script that I prepared uses your current prepdb.py script. the mini pipeline flow-work: 1. read input values: * fasta filename (nucleotide) * blast format: blast format: F->nucleotide, T->protein * database output name * fasta sequence IDs format (ncbi-gbk , other) where: ncbi-gbk means something like ">gi|gi-number|gb|accesión|locus" other means something like ">my own IDs" 2. if fasta sequence IDs are like ncbi format(ncbi-gk) then execute prepdb.py python script and generate new fasta file then go step 4 example: >gi|gi-number|gb|accesión|locus 3. if fasta sequence IDs has diferent (other) identifiers set to galaxy format first then execute prepdb.py python script then go step 4 >my own identifier 4. to format database using formatdb blast utility 5. setting up Megablast Galaxy Loc File 5. delete temp files 6. done Usage example: query help: ./set_galaxy_blastdb.sh -help format blast nucleotide dabatabase yeast, set galaxy loc file ./set_galaxy_blastdb.sh -fasta /media/xlinux/genomes/galaxy/palomero/megablast/yeast_nt.fasta -p F -n yeastdb -fastadesc ncbi-gk when script finished we have following results: $ls /media/xlinux/genomes/galaxy/palomero/megablast/ blastdb.loc new.yeast_nt.fasta yeastdb.nhr yeastdb.nin yeastdb.nsq yeast_nt.fasta How can I contribute with this shell script ? Thanks in advance -- Jacob http://www.langebio.cinvestav.mx/bioinformatica/jacob -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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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

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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

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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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Defining new file formats in Galaxy (for new tool wrappers)
by Peter Cock 15 Aug '11

15 Aug '11

Hi all, Something I've not needed to do until now is define a new file format in Galaxy. I understand the basic principle and defining a subclass in Python... however, how does this work with new tools on the Tool Shed? In particular, if an output format is likely to be used by more than one tool, can we get it added to the Galaxy core? As an example, the basic functionality of the Blast2GO for pipelines tool (b2g4pipe) takes a BLAST XML input file, and gives a tab separated annotation output file. Galaxy already has 'blastxml' and 'tabular' file formats defined, so I didn't need to do anything extra. However, the tool can also take (a directory of) InterProScan XML files as input, so here a new 'interproscanxml' format would useful. Then any wrapper using or producing InterProScan XML could take advantage of this. e.g. Konrad's InterProScan wrapper could then offer the XML output as an option in addition to or instead of the tabular output. Related to this example, why isn't there a generic base class for XML formats in general? https://bitbucket.org/galaxy/galaxy-central/issue/568/missing-xml-datatype-… Regards, Peter

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Request for pulling the updated FASTQ (de-)interlacer tool
by Florent Angly 05 Aug '11

05 Aug '11

Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository: https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent

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minor bug: double-quotes in dataset name
by Assaf Gordon 01 Aug '11

01 Aug '11

Hello, There's a small bug when entering a double-quote character in a dataset name: The double-quote confuses some later-on processing (templates and Display-Application XML), resulting in some problems. Example: This history has one BAM dataset with a name of: Hello "world" http://main.g2.bx.psu.edu/u/foobar/h/double-quotes-bug If you try to rename it (by clicking the "pencil" icon), you'll see only the "hello" part. If you try to load the BAM to the UCSC Genome browser, it will fail with this error message: Missing bigDataUrl setting from track of type=bam (Hello ) -gordon

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visual cue for <conditional> group parameters
by Assaf Gordon 01 Aug '11

01 Aug '11

Hi, The following tiny patch adds a light-gray visual cue in the html form, to give a better idea as to which parameters go together. It looks acceptable even with nested <conditional> parameters. See it in action here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_bowtie_pe1 http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1 It might not be the prettiest thing, but it works nicely with minimal code changes. Patch is here: http://cancan.cshl.edu/labmembers/gordon/files/conditional-group-css2.patch Comments are welcomed, -gordon

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