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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 07 Oct '16

07 Oct '16

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Modifying Values in the Database
by Katherine Beaulieu 04 Oct '16

04 Oct '16

Hello Everyone, I am trying to create a query to modify a value from a table in the galaxy database, but don't quite know what this language is that is being used to modify the database. The only command I know of are sa_session.add and sa_session.flush. Any help would be really appreciated! Katherine

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R dependency problems with readline libraries
by Nikolaos Tur 03 Oct '16

03 Oct '16

Hi, installation of deseq2 1.10.0 causes next problem: /home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory Installed tool dependencies: deseq2 R 3.2.1 installed without problems readline 6.3 installed too why does it happen? Is something missing? The same readline dependency problem from R happen also during installation of packages bioconductor_limma & bioconductor_edger Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown warnings and also related to R: /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libgfortran.so.1, needed by /home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link) /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libreadline.so.6, needed by /home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link) Thanx, Nikolaos

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building indexes
by Nikolaos Tur 03 Oct '16

03 Oct '16

Hi, I try to build indexes for ch38 (GRCh38.84 Toplevel) using data managers for BWA-MEM and TwoBit. Both failed. Error building index: Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit format does not support indexes larger than 4Gb, please split up into smaller files. [bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 46629609168 bytes at bwtindex.c line 135: Cannot allocate memory Error building index. So, how to split genome for TwoBit and how much RAM is needed for BWA indexes? These errors are from runs on machine with 45GB RAM. Thanx, Nikolaos

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Install error of package_bioconductor_limma_3_28_10
by Alexandre Defelicibus 03 Oct '16

03 Oct '16

Hi all, I got this error when I tried to install the package package_bioconductor_limma_3_28_10 <https://toolshed.g2.bx.psu.edu/repository/browse_repositories?sort=name&ope…> : Error downloading from URL https://depot.galaxyproject.org/software/limma/limma_3.28.10_src_all.tar.gz: HTTP Error 404: Not Found Could someone help me? Best regards, Alexandre

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