October 2016 - galaxy-dev - lists.galaxyproject.org

There is a bug in Lefse system
by Bueno Silva,Carla Grazielle 13 Oct '16

13 Oct '16

Hi! I'm trying to upload my data in Lefse system, but it show this message: "Failed: Bad Request (400)" Yesterday I tried and I could upload these files, but today I can not upload the same files. I think it's a problem in the website. Could you please help me? Thank you! =) Carla.

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Local galaxy reading shed_tool_conf xml section in reverse
by evan clark 12 Oct '16

12 Oct '16

I have modified the shed tool conf xml in order to add labels to tool sections and it appears to now be reading the xml in reverse and ordering the tools in the tool panel incorrectly. Image of issue: https://www.dropbox.com/s/rxbr2tpqkpeeysw/Screen%20Shot%202016-10-12%20at%2… ~~~~ <?xml version="1.0"?> <toolbox tool_path="../shed_tools"> <section id="hts:_rna_analysis" name="HTS: RNA Analysis" version=""> <label id="mapping" text="Mapping" /> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/758594ed0364/tophat2/tophat2_w…" guid="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>tophat2</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>758594ed0364</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0</id> <version>2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/1eb21dccc2fa/hisat2/hisat2.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>hisat2</repository_name> <repository_owner>iuc</repository_owner> <installed_changeset_revision>1eb21dccc2fa</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3</id> <version>2.0.3</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/ace9f5a2b40f/rgrnastar/rg_rnaSta…" guid="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>rgrnastar</repository_name> <repository_owner>iuc</repository_owner> <installed_changeset_revision>ace9f5a2b40f</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2</id> <version>2.4.0d-2</version> </tool> <label id="cuf_lnks" text="Cufflinks" /> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/b77178f66fc3/cuffcompare/c…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffcompare</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>b77178f66fc3</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/986b63735a5e/cuffquant/cuffq…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffquant</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>986b63735a5e</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/8160c8ea4eb9/cuffmerge/cuffm…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffmerge</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>8160c8ea4eb9</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/a26af05ac218/cuffnorm/cuffnor…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffnorm</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>a26af05ac218</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/9aab29e159a7/cufflinks/cuffl…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cufflinks</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>9aab29e159a7</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7</id> <version>0.0.7</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/0f32ad418df8/cuffdiff/cuffdif…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffdiff</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>0f32ad418df8</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3</id> <version>2.2.1.3</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/a1ea9af8d5f4/cufflinks/cuffl…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cufflinks</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>a1ea9af8d5f4</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/7d4c2097aac5/cuffnorm/cuffnor…" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.1"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffnorm</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>7d4c2097aac5</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.1</id> <version>2.2.1.1</version> </tool> </section> ~~~~

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troubles with galaxy database...
by Alexis Dereeper 10 Oct '16

10 Oct '16

Hi all, We are faced with some incomprehensible troubles with our Galaxy instance (newly upgraded to 16.07, using SGE and PostgreSQL database). Since two weeks, it started to suddenly give different kind of error messages randomly, sometimes it gives "failure preparing job", sometimes "The cluster DRM system terminated this job", sometimes it finishes without error, even when relaunching the same wrapper with the same input datasets. In parallel, we have a dev instance for which we do not have these troubles. The config files are substancially the same, except the connection to the database which is obviously different. We suspected an issue from PostgreSQL database. So we did some tests and changed the connection with an empty postgresql databse and the troubles seem to disappear. Is there any scripts to check the integrity of the database? Any recommendations to face this kind of troubles? It seems that there is inconsistencies in the database that makes the system crash. Thanks a lot for your help. Regards, Alexis -- Alexis DEREEPER UMR IPME (IRD-UM2-CIRAD) Interactions Plantes Microorganismes Environnement IRD - Institut de Recherche pour le Développement Bureau 351 911, avenue Agropolis BP 64501 34394 MONTPELLIER CEDEX 5 FRANCE Alexis.Dereeper(a)ird.fr tel IRD : + 33 (0)4 67 41 61 88 tel CIRAD : + 33 (0)4 67 61 57 21

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Budgeting a production Galaxy instance
by Vladimir Gritsenko 08 Oct '16

08 Oct '16

Hello all, We (at Tel Aviv University) are considering setting up a Galaxy instance (private, but production-geared). The capacity planning pages and surveys are great for hardware budgeting, but I want to ask about manpower. We’re looking forward to roughly 50 active users, and we’ll need to provide troubleshooting, training and integrating and writing new tools. In your experience, what is be the scope of a Galaxy admin’s position? Part-time? Full-time? Something else? Is more than one person needed to handle everything? Thank you, Vladimir Gritsenko

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Help wanted: setting up a production server
by Steve Cassidy 07 Oct '16

07 Oct '16

Hi all, I’m working on setting up a Galaxy server for use with speech and language data. While I can probably get there myself eventually, I’m thinking it would be good to get some (paid) help if it were available. If you have some experience setting up a public facing Galaxy instance, and you have some time available in the next couple of weeks, please get in touch. Any location is probably ok as long as we can work out how to reimburse you. We (and the servers) are based in Australia but I’m currently in New York. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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galaxy - bioperl - prokka
by Fernandez Edgar 07 Oct '16

07 Oct '16

Hello, I have installed prokka, perl and bioperl in my Galaxy's ToolShed. However, my users are getting this error during execution of prokka: Can't locate Bio/Root/Version.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka line 29. BEGIN failed--compilation aborted at /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka line 29. I was under the impression that the galaxy's tools will use the internal perl. Do I just need to install Bio::Root:Version on my system installation of perl? Please give me whatever information you can on this issue. Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568

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planemo test with <options from_data_table>
by D K 07 Oct '16

07 Oct '16

Hi galaxy-dev, I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo: 'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n >From my script XML: > <param name="refGenomeSource_type" type="select" label="Select a > reference genome / transcriptome"> > <options from_data_table="type_indexes"> > </options> > </param> > ... > <tests> > <test> > <param name="refGenomeSource_type" value="hsapiens"/> > </test> > </tests> > > From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored) > <table name="type_indexes" comment_char="#" > allow_duplicate_entries="False"> > <columns>value, name, path</columns> > <file path="tool-data/twobit.loc" /> > </table> and from twobit.loc (where the columns are tab separated): > hsapiens H. sapiens (hg38) > /remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa Any suggestions would be greatly appreciated!

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Fwd: [mailinglist] Call for Submissions: Computer Demo Track at PAGXXV.
by Dave Clements 07 Oct '16

07 Oct '16

Hi All, Computer demo submissions for Plant and Animal Genome are due October 28. See below for details. Galaxy will again have a presence at PAG. The two-hour Galaxy workshop on Tuesday will likely focus on genome annotation, and several other proposals are in the works. PAG is in San Diego in January. Hope to see you there, Dave C ---------- Forwarded message ---------- From: Monica Munoz-Torres <mcmunozt(a)lbl.gov> Date: Fri, Oct 7, 2016 at 3:15 AM Subject: [mailinglist] Call for Submissions: Computer Demo Track at PAGXXV. To: mailinglist(a)biocurator.org Cc: Monica Munoz-Torres <McMunozT(a)lbl.gov>, Brian Smith-White < smtwhite(a)ncbi.nlm.nih.gov> Dear Colleagues, *International Plant and Animal Genome XXV (PAGXXV)* *January 14-18, 2017. San Diego, California, United States.* http://intlpag.org/ PAGXXV will bring together more than 3,000 leading researchers in plant and animal research, over 130 exhibits, more than 150 workshops, over 1000 posters, *and a computer demo track specifically designed to highlight relevant software and online resources.* PAG is the largest Ag-Genomics meeting in the world. If you work on digital resources that enable life sciences research, please consider submitting an abstract to the PAG Computer Demonstration Track. Computer demos are 15 or 20 minutes long, and are an excellent way to get resources in front of the people who will benefit the most from them. *The Computer Demo abstract submission deadline is Friday October 28, 2016. * All computer demo presenters must be registered for the conference prior to submitting. Any software which is demonstrated at the PAG Conference must also be available to the scientific community and non-commercial. Visit http://www.intlpag.org/2017/abstracts/computer-demos for additional information and to find a link to the submission form. We hope to see you in San Diego! *Monica Munoz-Torres and Brian Smith-White* *PAGXXV Computer Demo Track Co-Chairs* [image: Inline image 1] -- Mentorship Matters! -- Monica Munoz-Torres, PhD. Berkeley Bioinformatics Open-source Projects (BBOP) Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Mailing Address: Lawrence Berkeley National Laboratory 1 Cyclotron Road Mailstop 977 Berkeley, CA 94720 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [galaxy-dev] planemo test with <options from_data_table>
by Peter Cock 07 Oct '16

07 Oct '16

Good, because you are using planemo test --galaxy_root ... you can preset the *.loc files as needed (because currently Planemo will not do this for you). See also Nicola's reply. Peter On Fri, Oct 7, 2016 at 5:49 PM, D K <danielfortin86(a)gmail.com> wrote: > Hi Peter, > > This is the command I'm using to run planemo: > . galaxy_test/.venv/bin/activate > planemo test --test_data /home/galaxy-functional-testdata --galaxy_root > galaxy-test/ --skip_venv test.xml > > I'm getting no errors when using the planemo lint tool. > > Thanks! > > On Fri, Oct 7, 2016 at 2:06 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: >> >> Hi DK, >> >> Looking at your XML that looks OK. >> >> It might not be important, but how exactly are you running planemo >> test? >> >> I'm asking because currently it will not create tool-data/twobit.loc >> for you from your sample file - although in that case I would have >> expected a different error message: >> >> https://github.com/galaxyproject/planemo/issues/530 >> https://github.com/galaxyproject/planemo/issues/530 >> >> Is planemo lint happy with your tool? >> >> Peter >> >> >> On Thu, Oct 6, 2016 at 11:08 PM, D K <danielfortin86(a)gmail.com> wrote: >>> >>> Hi galaxy-dev, >>> >>> I'm having a problem running a test using planemo where I would like the >>> value of a parameter taken from one of the data tables. I get the following >>> error in planemo: >>> >>> 'Error creating a job for these tool inputs - Parameter >>> refGenomeSource_type requires a value, but has no legal values defined.\n >>> >>> >>> From my script XML: >>>> >>>> <param name="refGenomeSource_type" type="select" label="Select a >>>> reference genome / transcriptome"> >>>> <options from_data_table="type_indexes"> >>>> </options> >>>> </param> >>>> ... >>>> <tests> >>>> <test> >>>> <param name="refGenomeSource_type" value="hsapiens"/> >>>> </test> >>>> </tests> >>>> >>> From my "tool_data_table_conf.xml.sample" and >>> "tool_data_table_conf.xml.test" (mirrored) >>>> >>>> <table name="type_indexes" comment_char="#" >>>> allow_duplicate_entries="False"> >>>> <columns>value, name, path</columns> >>>> <file path="tool-data/twobit.loc" /> >>>> </table> >>> >>> >>> and from twobit.loc (where the columns are tab separated): >>>> >>>> hsapiens H. sapiens (hg38) >>>> /remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa >>> >>> >>> Any suggestions would be greatly appreciated! >>> >>> >>> ___________________________________________________________ >>> 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: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> >> >

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Bioinformatics Trainings & Project Works
by Mohammed Iftekhar 06 Oct '16

06 Oct '16

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