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

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 04 Oct '16

04 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 04 Oct '16

04 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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News of the Galaxy: October 2016
by Dave Clements 03 Oct '16

03 Oct '16

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New Galaxy Australia community opens registrations for GAMe 2017
by Dave Clements 03 Oct '16

03 Oct '16

>From the GAMe 2017 Organising Committee <https://www.embl-abr.org.au/game2017/organisers/>: Today we officially launch the Galaxy Australia <https://www.embl-abr.org.au/galaxyaustralia/> community with the opening of registrations for the Galaxy Australasia Meeting 2017 (GAMe 2017) being held in Melbourne over 3-9 February. Australian Galaxy users and administrators will now have more opportunities to interact and collaborate to identify and address the needs of the local community. The community will also be a hub for Australian Galaxy training courses and offer a catalog of Australian Galaxy servers. The establishment of Galaxy Australia is supported by the EMBL Australia Bioinformatics Resource (EMBL-ABR) in its appointed role of supporting the development of skills and training in the Australian life science research community. At the EMBL-ABR Hub, hosted at the Victorian Life Sciences Computation Initiative (VLSCI), Galaxy is used extensively for teaching and data analysis directly as well as through the Australian-made Genomics Virtual Laboratory <https://www.genome.edu.au/>. VLSCI’s expert bioinformaticians and professional staff will help promote community activities and training. Galaxy Australia has a Twitter feed (@GalaxyAustralia <https://twitter.com/galaxyaustralia>) for announcements and discussion relevant to the community. *Galaxy Australasia Meeting 2017 (GAMe 2017)* The Community’s first major activity is to organise the Galaxy Australasia Meeting 2017 (GAMe 2017), 3-9 February in Melbourne. We are pleased to announce that early registration <https://www.embl-abr.org.au/game2017/registration/> and talk and poster abstract submission <https://www.embl-abr.org.au/game2017/submit-your-talkposter/> are now open for the GAMe 2017. This meeting will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia to share expertise across many levels. The conference <https://www.embl-abr.org.au/game2017/conference/> starts 4 February and features two full days of keynotes, accepted and sponsor talks, poster and sponsor sessions, birds-of-a-feather gatherings, a conference dinner and lots of opportunities for networking. Prior to the conference we are offering a Researcher Training Day <https://www.embl-abr.org.au/game2017/training-day/> on 3 February, aimed at biomedical researchers who need to analyse their biological data. The conference is followed by a four day workshop on Galaxy server administration <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> for those working at that level. Talk abstracts are due 30 November <https://www.embl-abr.org.au/game2017/submit-your-talkposter/> and early registration ends 31 December <https://www.embl-abr.org.au/game2017/registration/>. Register now and save up to 43% off regular registration rates. There are also scholarships available for eligible students and postdocs <https://www.embl-abr.org.au/game2017/registration/#scholarships>. The scholarship application deadline is 18 November. We look forward to welcoming you to Melbourne. Remember to pack for our fabulous February weather! *GAMe 2017 Organising Committee <https://www.embl-abr.org.au/game2017/organisers/> (#game_2017)* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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