October 2014 - galaxy-dev - lists.galaxyproject.org

Stop autoselecting in drop-down menus
by Aleksey Jironkin 18 Dec '14

18 Dec '14

Hi, I was wondering if there is a way to prevent auto-selecting an option for Running a workflow? Quiet often users (especially novices) would re-run workflows without checking much the data that goes in thinking it will be the same as before. But because the options in drop down menus are auto-populated it seems the top option is always selected by default. For example, previously we had a single fasta file as reference and in the process of a workflow few other fasta files get generated. they appear above the previous fasta in the selection, so without paying attention people skip the input without really checking it. Can we manually add a "blank" selection at the top to force users to select something? Alex -- Dr Aleksey Jironkin Bioinformatician Bioinformatics Unit Infectious Disease Informatics Microbiologicy Services, Colindale Public Health England 61 Colindale Avenue London NW9 5EQ Aleksey.Jironkin(a)phe.gov.uk Tel: 020 83 276610 www.gov.uk/phe Follow us on Twitter @PHE_uk Protecting and improving the nation’s health

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Strange issue with datatypes in Galaxy version of last week
by Lukasse, Pieter 12 Dec '14

12 Dec '14

Hi, Apparently a new datatypes bug has been introduced in the Galaxy version of last week: I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/> The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/> At first Galaxy output seems fine: [cid:image001.png@01CF4847.DE4A1A70] But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]- When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv . Anyone faced this issue? Thanks and regards, Pieter. Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Tool Shed Categories
by Alam, Khalid K. (MU-Student) 09 Dec '14

09 Dec '14

Hi; I’m getting ready to submit several (5) tools for processing data related to combinatorial selection technologies (aptamer and (deoxy)ribozyme selections, phage display, etc.) and would like to propose a new category for the Tool Shed entitled “Combinatorial Selections” where these repositories can be published. Khalid Kamal Alam University of Missouri Department of Biochemistry 415 Life Sciences Center 1201 Rollins St. Columbia, MO 65211 <mailto:khalidkalam@mail.missouri.edu>KhalidKAlam<mailto:KhalidKAlam@mail.missouri.edu>@mail.missouri.edu<mailto:kkafy3@mail.missouri.edu> @BiochemPhD

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datatype dependencies
by Eric Rasche 28 Nov '14

28 Nov '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Let's pretend for a second that I'm rather lazy (oh...wait), and I have ZERO interest in writing datatype parsers to sniff and validate whether or not a specific file is a specific datatype. I'm a sysadmin and bioinformatician, and I've worked with dozens of libraries that exist to parse file formats, and they all die in flames when I feed them bad data. Would it be possible to somehow define requirements for datatypes? I don't want to take on the burden of code I write saying "yes, I've sniffed+validated this and it is absolutely a genbank file". That's a lot of responsibility, especially if people have malformed genbank files and their tools fail as a result. I would like to do this with BioPython and turf the validation to another library that exists to parse genbank files, that will raise and exception if they're invalid. > def sniff(self, filename): > from Bio import SeqIO > try: > self.records = list(SeqIO.parse( filename, "genbank" )) > return True > except: > self.records = None > return False > > def validate(self, dataset): > from Bio import SeqIO > errors = list() > try: > self.records = list(SeqIO.parse( dataset.file_name, "genbank" )) > except Exception, e: > errors.append(e) > return errors > > def set_meta(self, dataset, **kwd): > if self.records is not None: > dataset.metadata.number_of_sequences = len(self.records) so much easier! And I can shift the burden of validation and sniffing to upstream, rather than any failures being my fault and requiring maintenance of a complex sniffer. Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTyBmyAAoJEMqDXdrsMcpVQa0P/jj0edAKM6QsodhRWHglR92W tej1tJjtPgtJ15wsFzq6wVfhbL5J39ytsWjjtk//jhVNXh4FEE/OFZe6Nx9uTFKP ybazyTrLSCrxsST+w+Rx8Q9vfzShr87vjP+fC1k5i2EZOgogPOcQml1ouOHHjC6z pArrwPOvL3ZxWJG7oEcZjUjrPD8+ffhfQ/x096YYIMw7Hg74d50ARwtawJRoslZD JnYWa+aUOcsvC3QMrLKkDm4qBaTHa5x7x7P07Lcx7X65iMPDcuMZNtImiLztNscF QwbbdJdcs8oeSRRnmKgAllRAKf4dMeiyaSI+muVzNlpvLlSMZBNawD0bO1OXmIQH vAaV0eU+rYmDJSGo330o+RydvlDJENTXOkDt0TxmvfYAPtg2TlJCiWUdL7V1LqqF n8J5Z7Cu/sqRGSr5ww6KY27QHq6TU1WZDsVZiyEWJeKg3HGzp0MUmzMdr7iSZawK gnZxv6qg3+FlSqA30niyAuxEq588vS8uEFjjOfhnNLsUM7FAuFANF5z9bPOhG2qM Xjc3/NY7NsERd9nsIwfRuz0DWni8upvZ39vfeRZ3OAW9NwjRzqXrQiQp08XHa934 z4EBnpcWc9rNSV/3APF/imecBTOoiKtZfzIfILLtOPGE407Bmd8cE8hWyW7ipvrT QU6DIimj3eoMn+elXDfX =M+s5 -----END PGP SIGNATURE-----

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Is anyone using composite datatype uploads?
by Aysam Guerler 25 Nov '14

25 Nov '14

Hello everyone, We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel > Get Data > Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet. Please let us know if you are using the composite file upload functionality of the former tool form. Thanks, Sam

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Re: [galaxy-dev] Some plugin for digital normalization
by Michael R. Crusoe 24 Nov '14

24 Nov '14

> From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com> > Date: December 26, 2013 2:37 AM > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] Some plugin for digital normalization > Hello all, > > I've been searching in tool sheds(main and test) for a plugin to do digital normalization of reads, for example Trinity has one script to do this (./util/normalize_by_kmer_coverage.pl), diginorm is another alternative (http://ged.msu.edu/papers/2012-diginorm/) > > Do you know if there is a galaxy tool ready for this work or should I develop my own? Hello Cristian, I am actively working on a wrapper for normalize-by-median.py and the other tools in the khmer suite. https://github.com/ged-lab/khmer/blob/galaxy-integration/scripts/normalize-… It requires some changes on our end which you can track here: https://github.com/ged-lab/khmer/pull/237 You can install this branch of khmer via pip pip install -e git+git@github.com:ged-lab/khmer.git@output_naming1#egg=khmer or if you don't have a github account: pip install -e git+ https://github.com/ged-lab/khmer.git@output_naming1#egg=khmer (Instructions on installing using a virtualenv or on OS X are at: https://khmer.readthedocs.org/en/latest/install.html just substitute in the pertinent pip line from above) I haven't tested it much; doing so is the top of my to-do list for the rest of this week. If you or anyone else is feeling adventurous I would be happy to have the feedback. Cheers! -- Michael R. Crusoe: Software Engineer and Bioinformatician mcrusoe(a)msu.edu @ the Genomics, Evolution, and Development lab; Michigan State University http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe

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Jobs stuck in "new" state - Data Library datasets to blame?
by Lance Parsons 14 Nov '14

14 Nov '14

Recently, I updated our Galaxy instance to use two processes (one for web, the other as a job handler). This has been working well, except in a few cases. I've noticed that a number of jobs get stuck in the "new" status. In a number of cases, I've resolved the issue by downloading and uploading one of the input files and rerunning the job using the newly uploaded file. In at least one of these cases, the offending input file was one that was copied from a Data Library. Can anyone point me to something to look for in the database, etc. that would cause a job to think a dataset was not ready for use as a job input? I'd very much like to fix these datasets since having to re-upload data libraries would be very tedious. Thanks in advance. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Tool shed environment dependency - HOW TO do this?
by Lukasse, Pieter 12 Nov '14

12 Nov '14

Hi, I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot use the "setup_r_environment" trick. I already got a tool_dependency.xml working that installs R 3.1.1 and the necessary Bioconductor packages using bioclite method (see attachment). Now my question is: * I would like to split up this into two steps as I don't want to trigger the compilation of new R environment every time I when I need to just update the Bioconductor package....the question is: how to do such things in general? How can I access the INSTALL_DIR of another tool from within another tool_dependency.xml? If I can do this, then my problem is solved. Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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bowtie2: no stderr output
by Elizabeth Chia 09 Nov '14

09 Nov '14

Dear all Usually the alignment statistics from bowtie2 will be printed to the stderr file, however, on the local instance, the stderr file is empty after alignment. It still does the alignment, but the statistics are not printed out. This is my hg summary: parent: 13802:f7dd0060c296 latest_2014.06.02 Merged in dannon/galaxy-central-prmaker/stable (pull request #404) branch: stable commit: 288 modified, 357 added, 18 unknown (new branch head) update: 27 new changesets (update) Will updating to the latest version help? Or are there any patches available? Thanks. Regards liz

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strange issue with .RData files
by Lukasse, Pieter 06 Nov '14

06 Nov '14

Hi, When I upload any .RData file to my Galaxy server it seems to be unpacking/changing it. The resulting file in my history is different and around 2x larger than the uploaded file. The tool that needs to use it also aborts with an error due to this erroneous file. What are the workarounds? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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