February 2013 - galaxy-dev - lists.galaxyproject.org

Test data for tophat2 with hg19 reference genome
by Sachit Adhikari 20 Feb '13

20 Feb '13

Hi, I need a test_data for Tophat with the hg19 reference genome? The test_data from this website http://tophat.cbcb.umd.edu/downloads/ doesn't have anything for hg19 reference genome. Where can I get the test data? Thanks

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Installing Prebuilt Indexes for "Tophat for Illumina" - What to do for color space files?
by greg 20 Feb '13

20 Feb '13

Hi, I'm trying to install DM3 from this page (http://tophat.cbcb.umd.edu/igenomes.html) as a pre-built index for "Tophat for Illumina" in our local galaxy install. I'm following the instructions on this page: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I see where I would use the *.ebwt files in the bowtie_index.loc file. But I'm not sure what to reference in the bowtie_index_color.loc file? (The same *.ebwt files??) Thanks, Greg (I asked this question on the tophat support site too, but on second look I think it was only for bug reports) For reference, here's what I downloaded from the DM3 file: Drosophila_melanogaster └── UCSC └── dm3 ├── Annotation │ ├── Archives │ │ ├── archive-2010-09-27-21-20-17 │ │ │ ├── ChromInfo.txt │ │ │ ├── cytoBand.txt │ │ │ ├── DATE.txt │ │ │ ├── genes.gtf │ │ │ ├── refFlat.txt │ │ │ ├── refFlat.txt.gz │ │ │ ├── refGene.txt │ │ │ ├── refMrna.fa │ │ │ ├── refSeqSummary.txt │ │ │ ├── splice_sites_34 │ │ │ │ ├── exon_coords.txt │ │ │ │ ├── splice_sites-34.fa │ │ │ │ ├── splice_sites-34.fa.2bpb │ │ │ │ ├── splice_sites-34.fa.idx │ │ │ │ └── splice_sites-34.fa.vld │ │ │ └── splice_sites_49 │ │ │ ├── exon_coords.txt │ │ │ ├── splice_sites-49.fa │ │ │ ├── splice_sites-49.fa.2bpb │ │ │ ├── splice_sites-49.fa.idx │ │ │ └── splice_sites-49.fa.vld │ │ ├── archive-2011-01-27-18-13-06 │ │ │ ├── Genes │ │ │ │ ├── ChromInfo.txt │ │ │ │ ├── cytoBand.txt │ │ │ │ ├── genes.gtf │ │ │ │ ├── refFlat.txt.gz │ │ │ │ ├── refGene.txt │ │ │ │ ├── refMrna.fa │ │ │ │ └── refSeqSummary.txt │ │ │ ├── README.txt │ │ │ ├── SmallRNA │ │ │ │ ├── hairpin.fa │ │ │ │ └── mature.fa │ │ │ └── Variation │ │ ├── archive-2011-08-30-21-29-02 │ │ │ ├── Genes │ │ │ │ ├── ChromInfo.txt │ │ │ │ ├── cytoBand.txt │ │ │ │ ├── genes.gtf │ │ │ │ ├── refFlat.txt.gz │ │ │ │ ├── refGene.txt │ │ │ │ └── refSeqSummary.txt │ │ │ ├── README.txt │ │ │ ├── SmallRNA │ │ │ │ ├── mature.fa │ │ │ │ └── precursor.fa │ │ │ └── Variation │ │ ├── archive-2012-03-09-03-02-51 │ │ │ ├── Genes │ │ │ │ ├── ChromInfo.txt │ │ │ │ ├── cytoBand.txt │ │ │ │ ├── genes.gtf │ │ │ │ ├── refFlat.txt.gz │ │ │ │ ├── refGene.txt │ │ │ │ └── refSeqSummary.txt │ │ │ ├── README.txt │ │ │ ├── SmallRNA │ │ │ │ ├── mature.fa │ │ │ │ └── precursor.fa │ │ │ └── Variation │ │ └── archive-current -> archive-2012-03-09-03-02-51 │ ├── Genes -> Archives/archive-2012-03-09-03-02-51/Genes │ ├── README.txt -> Archives/archive-2012-03-09-03-02-51/README.txt │ ├── SmallRNA -> Archives/archive-2012-03-09-03-02-51/SmallRNA │ └── Variation -> Archives/archive-2012-03-09-03-02-51/Variation ├── GenomeStudio │ ├── Archives │ │ ├── archive-2010-09-27-21-20-17 │ │ │ └── Drosophila_melanogaster │ │ │ └── UCSC-dm3_BDGP_rel5 │ │ │ ├── ChromInfo.txt -> ../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/ChromInfo.txt │ │ │ ├── cytoBand.txt -> ../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/cytoBand.txt │ │ │ ├── DATE.txt -> ../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/DATE.txt │ │ │ ├── refGene.txt -> ../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/refGene.txt │ │ │ ├── refMrna.fa -> ../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/refMrna.fa │ │ │ ├── refSeqSummary.txt -> ../../../../../Annotation/Archives/archive-2010-09-27-21-20-17/refSeqSummary.txt │ │ │ └── Sequence │ │ │ ├── chr2L.fa -> ../../../../../../Sequence/Chromosomes/chr2L.fa │ │ │ ├── chr2LHet.fa -> ../../../../../../Sequence/Chromosomes/chr2LHet.fa │ │ │ ├── chr2R.fa -> ../../../../../../Sequence/Chromosomes/chr2R.fa │ │ │ ├── chr2RHet.fa -> ../../../../../../Sequence/Chromosomes/chr2RHet.fa │ │ │ ├── chr3L.fa -> ../../../../../../Sequence/Chromosomes/chr3L.fa │ │ │ ├── chr3LHet.fa -> ../../../../../../Sequence/Chromosomes/chr3LHet.fa │ │ │ ├── chr3R.fa -> ../../../../../../Sequence/Chromosomes/chr3R.fa │ │ │ ├── chr3RHet.fa -> ../../../../../../Sequence/Chromosomes/chr3RHet.fa │ │ │ ├── chr4.fa -> ../../../../../../Sequence/Chromosomes/chr4.fa │ │ │ ├── chrM.fa -> ../../../../../../Sequence/Chromosomes/chrM.fa │ │ │ ├── chrX.fa -> ../../../../../../Sequence/Chromosomes/chrX.fa │ │ │ ├── chrXHet.fa -> ../../../../../../Sequence/Chromosomes/chrXHet.fa │ │ │ └── chrYHet.fa -> ../../../../../../Sequence/Chromosomes/chrYHet.fa │ │ ├── archive-2011-01-27-18-13-06 │ │ │ └── Drosophila_melanogaster │ │ │ └── UCSC-dm3 │ │ │ ├── ChromInfo.txt -> ../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/ChromInfo.txt │ │ │ ├── cytoBand.txt -> ../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/cytoBand.txt │ │ │ ├── refGene.txt -> ../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/refGene.txt │ │ │ ├── refMrna.fa -> ../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/refMrna.fa │ │ │ ├── refSeqSummary.txt -> ../../../../../Annotation/Archives/archive-2011-01-27-18-13-06/Genes/refSeqSummary.txt │ │ │ └── Sequence │ │ │ ├── chr2L.fa -> ../../../../../../Sequence/Chromosomes/chr2L.fa │ │ │ ├── chr2LHet.fa -> ../../../../../../Sequence/Chromosomes/chr2LHet.fa │ │ │ ├── chr2R.fa -> ../../../../../../Sequence/Chromosomes/chr2R.fa │ │ │ ├── chr2RHet.fa -> ../../../../../../Sequence/Chromosomes/chr2RHet.fa │ │ │ ├── chr3L.fa -> ../../../../../../Sequence/Chromosomes/chr3L.fa │ │ │ ├── chr3LHet.fa -> ../../../../../../Sequence/Chromosomes/chr3LHet.fa │ │ │ ├── chr3R.fa -> ../../../../../../Sequence/Chromosomes/chr3R.fa │ │ │ ├── chr3RHet.fa -> ../../../../../../Sequence/Chromosomes/chr3RHet.fa │ │ │ ├── chr4.fa -> ../../../../../../Sequence/Chromosomes/chr4.fa │ │ │ ├── chrM.fa -> ../../../../../../Sequence/Chromosomes/chrM.fa │ │ │ ├── chrX.fa -> ../../../../../../Sequence/Chromosomes/chrX.fa │ │ │ ├── chrXHet.fa -> ../../../../../../Sequence/Chromosomes/chrXHet.fa │ │ │ └── chrYHet.fa -> ../../../../../../Sequence/Chromosomes/chrYHet.fa │ │ ├── archive-2011-08-30-21-29-02 │ │ │ └── Drosophila_melanogaster │ │ │ └── UCSC-dm3 │ │ │ ├── ChromInfo.txt -> ../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/ChromInfo.txt │ │ │ ├── cytoBand.txt -> ../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/cytoBand.txt │ │ │ ├── refGene.txt -> ../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/refGene.txt │ │ │ ├── refSeqSummary.txt -> ../../../../../Annotation/Archives/archive-2011-08-30-21-29-02/Genes/refSeqSummary.txt │ │ │ └── Sequence │ │ │ ├── chr2L.fa -> ../../../../../../Sequence/Chromosomes/chr2L.fa │ │ │ ├── chr2LHet.fa -> ../../../../../../Sequence/Chromosomes/chr2LHet.fa │ │ │ ├── chr2R.fa -> ../../../../../../Sequence/Chromosomes/chr2R.fa │ │ │ ├── chr2RHet.fa -> ../../../../../../Sequence/Chromosomes/chr2RHet.fa │ │ │ ├── chr3L.fa -> ../../../../../../Sequence/Chromosomes/chr3L.fa │ │ │ ├── chr3LHet.fa -> ../../../../../../Sequence/Chromosomes/chr3LHet.fa │ │ │ ├── chr3R.fa -> ../../../../../../Sequence/Chromosomes/chr3R.fa │ │ │ ├── chr3RHet.fa -> ../../../../../../Sequence/Chromosomes/chr3RHet.fa │ │ │ ├── chr4.fa -> ../../../../../../Sequence/Chromosomes/chr4.fa │ │ │ ├── chrM.fa -> ../../../../../../Sequence/Chromosomes/chrM.fa │ │ │ ├── chrX.fa -> ../../../../../../Sequence/Chromosomes/chrX.fa │ │ │ ├── chrXHet.fa -> ../../../../../../Sequence/Chromosomes/chrXHet.fa │ │ │ └── chrYHet.fa -> ../../../../../../Sequence/Chromosomes/chrYHet.fa │ │ ├── archive-2012-03-09-03-02-51 │ │ │ └── Drosophila_melanogaster │ │ │ └── UCSC-dm3 │ │ │ ├── ChromInfo.txt -> ../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/ChromInfo.txt │ │ │ ├── cytoBand.txt -> ../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/cytoBand.txt │ │ │ ├── refGene.txt -> ../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/refGene.txt │ │ │ ├── refSeqSummary.txt -> ../../../../../Annotation/Archives/archive-2012-03-09-03-02-51/Genes/refSeqSummary.txt │ │ │ └── Sequence │ │ │ ├── chr2L.fa -> ../../../../../../Sequence/Chromosomes/chr2L.fa │ │ │ ├── chr2LHet.fa -> ../../../../../../Sequence/Chromosomes/chr2LHet.fa │ │ │ ├── chr2R.fa -> ../../../../../../Sequence/Chromosomes/chr2R.fa │ │ │ ├── chr2RHet.fa -> ../../../../../../Sequence/Chromosomes/chr2RHet.fa │ │ │ ├── chr3L.fa -> ../../../../../../Sequence/Chromosomes/chr3L.fa │ │ │ ├── chr3LHet.fa -> ../../../../../../Sequence/Chromosomes/chr3LHet.fa │ │ │ ├── chr3R.fa -> ../../../../../../Sequence/Chromosomes/chr3R.fa │ │ │ ├── chr3RHet.fa -> ../../../../../../Sequence/Chromosomes/chr3RHet.fa │ │ │ ├── chr4.fa -> ../../../../../../Sequence/Chromosomes/chr4.fa │ │ │ ├── chrM.fa -> ../../../../../../Sequence/Chromosomes/chrM.fa │ │ │ ├── chrX.fa -> ../../../../../../Sequence/Chromosomes/chrX.fa │ │ │ ├── chrXHet.fa -> ../../../../../../Sequence/Chromosomes/chrXHet.fa │ │ │ └── chrYHet.fa -> ../../../../../../Sequence/Chromosomes/chrYHet.fa │ │ └── archive-current -> archive-2012-03-09-03-02-51 │ ├── Drosophila_melanogaster -> Archives/archive-2012-03-09-03-02-51/Drosophila_melanogaster │ └── README.txt └── Sequence ├── AbundantSequences │ ├── adapter_contam1.fa │ ├── adapter_contam1.fa.2bpb │ ├── adapter_contam1.fa.vld │ ├── chrM.fa │ ├── chrM.fa.2bpb │ ├── chrM.fa.vld │ ├── phix.fa │ ├── phix.fa.2bpb │ ├── phix.fa.vld │ ├── polyA.fa │ ├── polyA.fa.2bpb │ ├── polyA.fa.vld │ ├── polyC.fa │ ├── polyC.fa.2bpb │ ├── polyC.fa.vld │ ├── ribosomal.fa │ ├── ribosomal.fa.2bpb │ └── ribosomal.fa.vld ├── Bowtie2Index │ ├── genome.1.bt2 │ ├── genome.2.bt2 │ ├── genome.3.bt2 │ ├── genome.4.bt2 │ ├── genome.fa -> ../WholeGenomeFasta/genome.fa │ ├── genome.rev.1.bt2 │ └── genome.rev.2.bt2 ├── BowtieIndex │ ├── genome.1.ebwt │ ├── genome.2.ebwt │ ├── genome.3.ebwt │ ├── genome.4.ebwt │ ├── genome.fa -> ../WholeGenomeFasta/genome.fa │ ├── genome.rev.1.ebwt │ └── genome.rev.2.ebwt ├── BWAIndex │ ├── genome.fa -> version0.6.0/genome.fa │ ├── genome.fa.amb -> version0.6.0/genome.fa.amb │ ├── genome.fa.ann -> version0.6.0/genome.fa.ann │ ├── genome.fa.bwt -> version0.6.0/genome.fa.bwt │ ├── genome.fa.pac -> version0.6.0/genome.fa.pac │ ├── genome.fa.sa -> version0.6.0/genome.fa.sa │ ├── version0.5.x │ │ ├── genome.fa -> ../../WholeGenomeFasta/genome.fa │ │ ├── genome.fa.amb │ │ ├── genome.fa.ann │ │ ├── genome.fa.bwt │ │ ├── genome.fa.pac │ │ ├── genome.fa.rbwt │ │ ├── genome.fa.rpac │ │ ├── genome.fa.rsa │ │ └── genome.fa.sa │ └── version0.6.0 │ ├── genome.fa -> ../../WholeGenomeFasta/genome.fa │ ├── genome.fa.amb │ ├── genome.fa.ann │ ├── genome.fa.bwt │ ├── genome.fa.pac │ └── genome.fa.sa ├── Chromosomes │ ├── chr2L.fa │ ├── chr2LHet.fa │ ├── chr2R.fa │ ├── chr2RHet.fa │ ├── chr3L.fa │ ├── chr3LHet.fa │ ├── chr3R.fa │ ├── chr3RHet.fa │ ├── chr4.fa │ ├── chrM.fa │ ├── chrX.fa │ ├── chrXHet.fa │ └── chrYHet.fa ├── Squashed-Drosophila_melanogaster-UCSC-dm3 │ ├── chr2L.fa -> ../Chromosomes/chr2L.fa │ ├── chr2L.fa.2bpb │ ├── chr2L.fa.vld │ ├── chr2LHet.fa -> ../Chromosomes/chr2LHet.fa │ ├── chr2LHet.fa.2bpb │ ├── chr2LHet.fa.vld │ ├── chr2R.fa -> ../Chromosomes/chr2R.fa │ ├── chr2R.fa.2bpb │ ├── chr2R.fa.vld │ ├── chr2RHet.fa -> ../Chromosomes/chr2RHet.fa │ ├── chr2RHet.fa.2bpb │ ├── chr2RHet.fa.vld │ ├── chr3L.fa -> ../Chromosomes/chr3L.fa │ ├── chr3L.fa.2bpb │ ├── chr3L.fa.vld │ ├── chr3LHet.fa -> ../Chromosomes/chr3LHet.fa │ ├── chr3LHet.fa.2bpb │ ├── chr3LHet.fa.vld │ ├── chr3R.fa -> ../Chromosomes/chr3R.fa │ ├── chr3R.fa.2bpb │ ├── chr3R.fa.vld │ ├── chr3RHet.fa -> ../Chromosomes/chr3RHet.fa │ ├── chr3RHet.fa.2bpb │ ├── chr3RHet.fa.vld │ ├── chr4.fa -> ../Chromosomes/chr4.fa │ ├── chr4.fa.2bpb │ ├── chr4.fa.vld │ ├── chrM.fa -> ../Chromosomes/chrM.fa │ ├── chrM.fa.2bpb │ ├── chrM.fa.vld │ ├── chrX.fa -> ../Chromosomes/chrX.fa │ ├── chrX.fa.2bpb │ ├── chrX.fa.vld │ ├── chrXHet.fa -> ../Chromosomes/chrXHet.fa │ ├── chrXHet.fa.2bpb │ ├── chrXHet.fa.vld │ ├── chrYHet.fa -> ../Chromosomes/chrYHet.fa │ ├── chrYHet.fa.2bpb │ └── chrYHet.fa.vld └── WholeGenomeFasta ├── genome.dict ├── genome.fa └── genome.fa.fai

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FastQC Question
by Min Cho 20 Feb '13

20 Feb '13

Hello, When trying to run FastQC, I get this error: Traceback (most recent call last): File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 162, in <module> html,retval,serr = f.run_fastqc() File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 63, in run_fastqc sout.write('# FastQC cl = \n' % ' '.join(cl)) TypeError: not all arguments converted during string formatting Is there anything I can do to modify the code to fix this? I'm using data run through FASTQ Groomer. Thank you

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galaxy-dev mailing list
by Oya Uyguner 20 Feb '13

20 Feb '13

I would like to enroll, galaxy-dev mailing list. Regards, Z. Oya Uyguner Department of Medical Genetics Istanbul Medical Faculty Istanbul University Bu elektronik posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafindan alinmasi amaçlanan yetkili gerçek ya da tüzel kisinin kullanimi içindir.Eger söz konusu yetkili alici degilseniz bu elektronik postanin içerigini açiklamaniz, kopyalamaniz, yönlendirmeniz ve kullanmaniz kesinlikle yasaktir ve bu elektronik postayi derhal silmeniz gerekmektedir. ISTANBUL ÜNIVERSITESI bu mesajin içerdigi bilgilerin dogrulugu veya eksiksiz oldugu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne sekilde olursa olsun içeriginden, iletilmesinden, alinmasindan ve saklanmasindan sorumlu degildir. Bu mesajdaki görüsler yalnizca gönderen kisiye aittir ve ISTANBUL ÜNIVERSITESI'nin görüslerini yansitmayabilir. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------! ----------------------- This message and attachments are confidential and intended solely for the individual(s) stated in this message.This email is not intended to impose nor shall it be construed as imposing any legally binding obligation upon ISTANBUL UNIVERSITY and/or any of its subsidiaries or associated companies. Neither ISTANBUL UNIVERSITY nor any of its subsidiaries or associated companies gives any representation or warranty as to the accuracy or completeness of the contents of this email. ISTANBUL UNIVERSITY will not be held liable to any person resulting from the use of any information contained in this email and will not be liable to any person who acts or omits to do anything in reliance upon it.

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environment variables and paths for toolshed tools
by David Hoover 20 Feb '13

20 Feb '13

Are there any environment variables that are honored by toolshed installed tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test toolshed, then installed it automatically. Neither of these resolved to what I expected. I don't want to hard-code the path in the xml tool file, but rather have a default location for other executables and jar files. How should this best be done? David Hoover Helix Systems Staff

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Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed
by Dannon Baker 20 Feb '13

20 Feb '13

On Feb 13, 2013, at 6:16 PM, David Joly <idjoly(a)gmail.com> wrote: > Hi! > > Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something. > > First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini? -Dannon

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not enough memory space on my galaxy session
by auguste aurelie 20 Feb '13

20 Feb '13

Dear Galaxy manager, I have a problem, I'm actually running my RNA seq project on your galaxy on line program. The matter is I do not have enough space. I'm running 12 times 3 to 4 mega bit of data. I have fews options: 1. running my samples in two times... which is quite difficult because they are all correlate 2. deleted the first files, like the first fastq files, but I'm affraid to have an error messages 3. to obtain more memory, just for the time of the study. Thanks a lot for your help -- *AUGUSTE Aurélie* Post doctorante Génétique et génomique du développement gonadique Université Paris-Diderot/Paris 7 Institut Jacques Monod CNRS-UMR 7592 555B - Bâtiment Buffon 15 Rue Hélène Brion Paris Cedex 13 France. Phone: 0033 1 57 27 81 17

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deleting and free space
by Hakeem Almabrazi 19 Feb '13

19 Feb '13

Hi, I have my own local galaxy installed and things are great. However, I am running of space, is there a better way to free space from the GUI? I have been deleting sets/files from my history but it looks like the Usage still going up. I manually run the following scripts but still nothing change There are 5 scripts included in the Galaxy distribution that can be used to clean up unwanted histories, libraries and datasets. There are located in the <GALAXY_ROOT>/scripts/cleanup_datasets directory and are named: * delete_userless_histories.sh * purge_histories.sh * purge_datasets.sh * purge_folders.sh * purge_libraries.sh * delete_datasets.sh Is there better ways to do this task? Regards,

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Merge internal head to release_2012.02.08
by Derrick Lin 19 Feb '13

19 Feb '13

Hi guys, We have checked in few internal changesets to our galaxy. Normally we did hg pull then hg merge for upgrading. With the 8 Feb release, it advice that we must do hg update release_2013.02.08 if we want to upgrade from stable branch. My understanding for hg update is, it will overwrite all local changes which we want to avoid. So in our case, what's the best way for us to upgrade? Cheers, Derrick

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Galaxy @ GMOD2013 & Biocuration 2013
by Dave Clements 19 Feb '13

19 Feb '13

Hello all, There are a couple of things going on with the GMOD Project<http://gmod.org/wiki/> that the Galaxy Community might be interested in. If you aren't familiar with GMOD, it is a federation of open-source projects and tools that enable visualizing, annotating, managing, and analyzing biological research data. GMOD includes Galaxy and several other widely used tools such as BioMart<http://gmod.org/wiki/BioMart> , InterMine <http://gmod.org/wiki/InterMine>, MAKER<http://gmod.org/wiki/MAKER> , Chado <http://gmod.org/wiki/Chado> and GBrowse<http://gmod.org/wiki/GBrowse> and JBrowse <http://gmod.org/wiki/JBrowse>. The first is that GMOD is running a community-wide survey<http://gmod.org/survey.html> through March 1. The survey "aims to find out how you are using GMOD, what you find useful (or otherwise), what support you need, and some information on the GMOD components you use." The survey results will be published at gmod.organd past surveys have been extremely useful to the project. If that's not enough motivation, once you are done with the survey, you can enter to win a free genome profile from 23andMe. - → *C'mon, take the dang survey <http://gmod.org/survey.html>.* The second is that registration is now open for the 2013 GMOD Meeting<http://gmod.org/wiki/April%202013%20GMOD%20Meeting> being held in Cambridge, UK, April 5 and 6. There will be a Galaxy presence (at least a project update, and I'm lobbying for a CloudMan<http://wiki.galaxyproject.org/CloudMan> workshop as well (and you could lobby too! <help(a)gmod.org>)). Finally, Biocuration 2013 <http://www.ebi.ac.uk/biocuration2013/home> is immediately after the GMOD Meeting, and also in Cambridge. Biocuration will feature a GO Galaxy Workshop<http://wiki.geneontology.org/index.php/GO_Galaxy_Workshop_at_Biocuration_20…> about using Galaxy to reason with ontologies. Thanks, Dave Clements -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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