- galaxy-dev - lists.galaxyproject.org

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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Re: [galaxy-dev] [galaxy-user] Megblast GIs
by Peter Cock 09 May '11

09 May '11

On Sat, May 7, 2011 at 12:01 AM, Douglas Rhoads <drhoads(a)uark.edu> wrote: > We have a local install of Galaxy and are using it for training grad and > undergrad students (using the Windshield Splatter data). We have a > relatively new install and the Megablast seems to be doing something funny > with the output in that column 2 which is supposed to be the GI of the > database hit is now two numbers joined with an underline (see below). I > need to tell my IT people what is wrong so they can correct the problem. > BL1-1-3 157649053_111750 91.30 46 4 0 10 55 58541 58496 2e- > 06 60.0 > BL1-1-5 161788633_175843 100.00 26 0 0 15 40 48812 48787 4e- > 04 52.0 Which version of BLAST do you have? If you're using the "megablast" tool in Galaxy, then it will be NCBI "legacy" BLAST using the blastall binary. If you're using the (commented out by default) BLAST+ wrappers, then it will be using the blastn binary. There were changes to the ID handling in the tabular output in BLAST 2.2.25+ as I recall. Another important factor is how the BLAST database was made (with or without the -parse_seqids flag). Peter P.S. Questions like this about local installs might be better on the galaxy-dev list, CC'd.

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question about Filtering Cufflink files
by shamsher jagat 09 May '11

09 May '11

Jeremy, I have been trying to follow the steps in filtering Cufflink out put files you have described in one of the previous messages ( http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put… ): I have shared histroy with you, but in summary: File 35: when Filter GTF data by attributes value list on data 11 (combined GTF) and data 33 (which is gene expr file) . Will not this should have one gene per row. But it is not? File 39: Filter GTF file by attribute value list on data 11 and data 38 (Cuffdiff splicing expr) it failed. I would assume that it should filter on the basis of TSSid . The error message is Traceback (most recent call last): File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 67, in filter( gff_file, attribute_name, ids_file, output_file ) File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 57, in filter if attributes[ attribute_name ] in ids_dict: KeyError: 'tss_id' 40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp) failed and error message is: Traceback (most recent call last): File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 67, in filter( gff_file, attribute_name, ids_file, output_file ) File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 57, in filter if attributes[ attribute_name ] in ids_dict: KeyError: 'tss_id' I would consider that if one gene has different Id than there is splicing . However in contrast isoform file with transcript Id is working fine (File 20) On a different note can I convert GTF file to txt tab delaminated file I tried to convert file 11 in txt (following Edit attributes) but the file is not properly formatted especially col-pid and TSS id. Am I doing something wrong. Thanks.

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Megablast GIs
by drhoads＠uark.edu 07 May '11

07 May '11

Message: 15Megblast GIs Date: Sat, 7 May 2011 12:00:19 +0100 From: Peter Cock <p.j.a.cock(a)googlemail.com> To: drhoads(a)uark.edu Cc: galaxy-user(a)lists.bx.psu.edu, Galaxy Dev <galaxy-dev(a)bx.psu.edu> Subject: Re: [galaxy-dev] [galaxy-user] Message-ID: <BANLkTin6W-bh2H1KYPBQ0YinxTzVU32XJQ(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Sat, May 7, 2011 at 12:01 AM, Douglas Rhoads <drhoads(a)uark.edu> wrote: > We have a local install of Galaxy and are using it for training grad and > undergrad students (using the Windshield Splatter data).? We have a > relatively new install and the Megablast seems to be doing something funny > with the output in that column 2 which is supposed to be the GI of the > database hit is now two numbers joined with an underline (see below).? I > need to tell my IT people what is wrong so they can correct the problem. > BL1-1-3?????157649053_111750?????91.30????????46?????????????4??????????????0??????????????10?????????????55?????????????58541???????58496???????2e- > 06?????????????60.0 > BL1-1-5?????161788633_175843?????100.00???????26?????????????0??????????????0??????????????15?????????????40?????????????48812???????48787???????4e- > 04?????????????52.0 Which version of BLAST do you have? If you're using the "megablast" tool in Galaxy, then it will be NCBI "legacy" BLAST using the blastall binary. If you're using the (commented out by default) BLAST+ wrappers, then it will be using the blastn binary. There were changes to the ID handling in the tabular output in BLAST 2.2.25+ as I recall. Another important factor is how the BLAST database was made (with or without the -parse_seqids flag). Peter P.S. Questions like this about local installs might be better on the galaxy-dev list, CC'd. ****************************** Thanks Peter, I debated which to post to. This is just using the Megablast tool in Galaxy. My IT people are not Biologists. They had this working fine and some tweak has screwed up the GI column in the results file. It should be the same NR and HTGS datafiles that we had before. So you recommend that I should just have them reinstall the databases and make sure to use the correct switches? Douglas Rhoads, Professor of Biological Sciences Director of Graduate Program in Cell and Molecular Biology 601 SCEN, Dept. of Biological Sciences, 1 University of Arkansas, Fayetteville, AR 72701 drhoads(at)uark.edu, http://biscweb.uark.edu/drhoads phone: 479-575-3251 FAX: 479-575-4010

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Re: [galaxy-dev] [galaxy-user] Composite Datatypes Q.
by Ross 07 May '11

07 May '11

Hi, Todd Composite datatypes work well to organise and present a bunch of outputs without cluttering up a history I think. The new picard tools in galaxy-central (only exposed on test right now) do this in various (complicated!) ways - eg take a look at the source for the gcbias tool https://bitbucket.org/galaxy/galaxy-central/src/43e581afb8a5/tools/picard/r… and https://bitbucket.org/galaxy/galaxy-central/src/43e581afb8a5/tools/picard/p… <https://bitbucket.org/galaxy/galaxy-central/src/43e581afb8a5/tools/picard/p…> I hope this helps give you a starting point for Galaxifying (or perhaps "engalaxying" !?) many new tools! (I'm moving this to galaxy-dev - probably more appropriate than galaxy-user...) On Fri, May 6, 2011 at 5:46 PM, Todd Yilk <tyilk(a)lanl.gov> wrote: > I have a program I'm trying to "galaxify" that emits a variable number of > result files. I would like the output of my Galaxy tool to show up in Galaxy > as an html file with links to the result files. So when you click on the > eye, the html file should up in the middle pane ... sorry if I'm not > describing this in an elegant way. > > Creating a composite datatype is the way to go in this situation, correct? > I'm creating a class that inherits from Html. How do I get the result > returned from my custom "generate_primary_file" function to show up as a > tool's output ... if that's the right way to go about this? > > Thanks! > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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Galaxy tools written in java
by Frederick van Staden 07 May '11

07 May '11

Hello! Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue. Anyone that could guide me in the right direction? Regards Frederick

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adding to the wiki
by Frederick van Staden 07 May '11

07 May '11

Is there a way i can contribute to the wiki? Regards Fred

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Bowtie why it does not take the 1_sequence.txt nor for bowtie nor the Convert
by Olivier Schaad 06 May '11

06 May '11

Dear Sir I try to use Bowtie mapping in galaxy , I import my Illumina s_1_sequence.txt , then I try to use the convert my userName is my email 21: FASTQ Groomer on data 9 An error occurred running this job: /There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have/ but I do have for all the files an error I upload the data using URL http://home.adm.unige.ch/~prnfg/HowardRiezman/wt(RH%20448)%20s_1_sequence.t… http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-1B%20erg3%209f-10A-1B%20s_… http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-9D%20erg3%2013f-9D-9D%20s… http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-13B%20erg3%2013f-9D-13B%2… http://home.adm.unige.ch/~prnfg/HowardRiezman/erg3%20RH%205702%20erg3%20s_1… http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-3A%20erg3%209f-10A-3A%20s_… Could you advice me ? Best regards

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