August 2013 - galaxy-user - lists.galaxyproject.org

Join the HOMER Galaxy wrapper development!
by Bjoern Gruening 13 Aug '13

13 Aug '13

Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc files to define different HOMER datasets - macros - compostite datatypes (html output) I think that project can be a good start to learn Galaxy Tool development with all its simple and enhanced features. Also HOMER is a complex suite and you can add small and really big features if you like. If you are interested but did not have any experience in Tool development, do not hesitate to ask. I will try to help and explain as much as I can. For the beginning I included only 3 tools, and only one of them with a bunch of parameters. So there are many things to do ... If anyone is interested in leaning Galaxy Tool development and want to contribute. Fell free to join and contact me. Cheers, Bjoern P.S. I do not mind to merge my changes to the already existing repository from Kevin, but I was not able to contact him. http://toolshed.g2.bx.psu.edu/view/kevyin/homer

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Galaxy Distribution Aug 12, 2013
by Jennifer Jackson 13 Aug '13

13 Aug '13

*Galaxy Distribution **Aug 12, 2013* / / /////http://bit.ly/galaxy20130812/ *Highlights:* * Upgrades to *Data Manager* including improved installation actions * *Visualization* Framework tunings, plus updates to *Phyloviz*, *Scatterplot*, and *Trackster *** * *Workflows* include new reproducibility controls and editing features * Multiple *Tool Shed* enhancements, features, and tunings * Plus additional updates to the *UI*, *Admin* and *Core*, and *API*, an important *Security Fix* reminder, and *Bug Fixes* http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2013.08.12 /Thanks for using Galaxy,/ The Galaxy Team -- Jennifer Hillman-Jackson http://galaxyproject.org

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how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini
by tin h 12 Aug '13

12 Aug '13

Hello galaxy gurus, I am trying to configure a local galaxy server to submit to SGE using DRMAA, it works, but I would like to specify the equivalent of "-v TMPDIR=/scratch" for qsub. I tried updating universe_wsgi.ini with something like: default_cluster_job_runner = drmaa://-q default.q -V -v TMPDIR=/scratch/ but that doesn't work because "/" is a delimiter, and I have not been able to find way to escape it. Is there any tricks for this? Much thanks in advance for your help in this matter. -Tin

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fastq file generated by SAMTOOLS can't be recognized
by Mark Edward Fabreag 09 Aug '13

09 Aug '13

Good day. I'm trying to use Galaxy's FASTQ to FASTA converter. However, the fastq file I generated using SAMTOOLS, can't be recognized. Hope you could help me with this problem. Thank you..

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Grooming on Galaxy
by Scott Tighe 08 Aug '13

08 Aug '13

Dear Galaxy Recently grooming has taken a few days. Is this typical? Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core University of Vermont Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2557 On 8/7/2013 3:37 AM, Fabrice BESNARD wrote: > Hi, > > Using SnpEff in the Galaxy main server, I need the Caenorhabditis briggsae > genome as a reference, which is not an option in the genome list given by > the tool as implemented in Galaxy right now. > > In the doc of SnpEff, it is said that this database is available > (c_briggsae_WS230, down-load link here : > http://sourceforge.net/projects/snpeff/files/databases/v3_3/) > However, the version of SnpEff in Galaxy is 1.0. It is said in the SnpEff > docs that the database version should match the SnpEff version > (http://snpeff.sourceforge.net/download.html) I found that the first > release of a C. briggsae database dates back to the version 2.1 of SnpEff > (See here: http://sourceforge.net/projects/snpeff/files/databases/v2_1/) > > Would it be to possible to up-date the list of databases of SnpEff in the > main server, to include the C. briggsae WS230? > If versions are not compatible, would it be possible to update SnpEff to a > more recent version? > > If this is not possible right now (I must confess I don't know how much > work this upddate would require), I guess the best and quickest > alternative option would be to install a SnpEff locally. Do you think it's > worth trying this, knowing that I don't feel very comfortable with > informatics (In other words, is the installation easy) ? > > many thanks in advance for your comments and advices, >

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(no subject)
by Meabh Beatty 08 Aug '13

08 Aug '13

I am new to Galaxy and am using it for analysis of BLAST results and phylogeny. I have uploaded a file with contig names, the BLAST GI number, and the total read count for each contig. When I use Galaxy to 'Summarize taxonomy' and 'Draw phylogeny', I have lost the total read counts. Eg. In the results of these it tells me how many contigs belong to Fungi or Metazoa, whereas each contig actually has a different number of reads. Is there any way to reflect this in Galaxy? I hope this makes sense!

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Downloading Output File thru FileZilla
by Mark Edward Fabreag 08 Aug '13

08 Aug '13

Good day. I just want to inquire if there is a way to download output through FileZilla. Thank you very much.

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Database of c_briggsae_WS230 for SnpEff
by Fabrice BESNARD 07 Aug '13

07 Aug '13

Hi, Using SnpEff in the Galaxy main server, I need the Caenorhabditis briggsae genome as a reference, which is not an option in the genome list given by the tool as implemented in Galaxy right now. In the doc of SnpEff, it is said that this database is available (c_briggsae_WS230, down-load link here : http://sourceforge.net/projects/snpeff/files/databases/v3_3/) However, the version of SnpEff in Galaxy is 1.0. It is said in the SnpEff docs that the database version should match the SnpEff version (http://snpeff.sourceforge.net/download.html) I found that the first release of a C. briggsae database dates back to the version 2.1 of SnpEff (See here: http://sourceforge.net/projects/snpeff/files/databases/v2_1/) Would it be to possible to up-date the list of databases of SnpEff in the main server, to include the C. briggsae WS230? If versions are not compatible, would it be possible to update SnpEff to a more recent version? If this is not possible right now (I must confess I don't know how much work this upddate would require), I guess the best and quickest alternative option would be to install a SnpEff locally. Do you think it's worth trying this, knowing that I don't feel very comfortable with informatics (In other words, is the installation easy) ? many thanks in advance for your comments and advices, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

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jobrunner upload file
by Jasper Jan Koehorst 07 Aug '13

07 Aug '13

Hello, I have a very simple jobrunner script that allows only 1 job to be run as this galaxy is used for one thing in particular which consumes almost all resources. To do this I set the following: <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/> </plugins> This works, but is it possible to create a second worker that is only allowed to be used for uploading files? So people can upload their data already and only enter the queue for the big analysis? Otherwise if they turn their computer off in the evening the upload is gone...

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FTP problem
by Karen Schwarzberg 07 Aug '13

07 Aug '13

Hello, I am using the Galaxy server and I am trying to upload files. I do not see the FTP option even when logged in. Please advise. Best regards, Karen

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