- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] trackster reference genome
by Jeremy Goecks 15 Aug '11

15 Aug '11

Colin, > How is it possible to preinstall a reference genome for trackster (hg19) within galaxy. > > i tried to find a dedicated help page but could not find any. Could you please link me to relevant information? See the section titled 'Setup for local instances' on this page: http://wiki.g2.bx.psu.edu/Learn/Visualization Finally, please send all emails to our mailing lists--in this case, galaxy-dev, which I've cc'd--rather than individual Galaxy developers or other list members. Sending email to the mailing lists ensures that everyone can see and contribute to questions and issues; in addition, emails to mailing lists are tracked and archived so that they are available in the future. Best, J.

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Picard installation problem
by colin molter 15 Aug '11

15 Aug '11

Hello all, I get troubles installing Picard. In short is there a dedicated link with precise instructions on how to install it on Galaxy? I spent hours trying to install it and if I made a subtle step forward in the installation, I am still stuck with exceptions when trying to run any picard tool. My first problem was to have a link to a built-in reference genome. I finally fixed it. I explain my solution here for interested persons. (1) create the 'dict' file from your reference fasta file by using the following picard tool: java -jar CreateSequenceDictionary.jar -R=<ref-genome.fa> -O=<ref-genome.dict> (2) modify the picard.loc index file to point to the correct location (3) -- the step that took me hours to find -- modify the all-fasta.loc file to point to the correct location. Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception: File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 class PicardBase(): ^ SyntaxError: invalid syntax I downloaded the last release of picard (picard-tools-1.48) and put all the jars file in tool-data/shared/jars/ permission of the files are : -rw-r--r-- 1 apache adm I suspect that galaxy can't find the jars file (i get the same error if I remove them from that location). Am I missing something? Should I precise something about the classpath in galaxY? Thank you for your help, Colin

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Extracting regions of sequences given table of co-ords
by Peter Cock 13 Aug '11

13 Aug '11

Hi all, I'm about to start working on a general tool for extracting sequences (from FASTA etc) based on a tabular file describing desired regions (this could be a BED or GFF3 file), giving a new sequence file with one entry for each region in the tabular file. Essentially I want as input columns describing: * FASTA sequence ID * Start * End * Strand (optional) * Region ID for this sequence in the output file (optional) In the case of a GFF3 input, those would be columns 1, 4, 5, 7 (with the ID being hidden inside column 9). But this isn't really driven by GFF3 where you'd probably not want to treat each line separately anyway (compound features). I'm thinking of very general examples like extracting general search matches (BLAST, HMMER, motifs, etc), but specifically things like cleaving proteins to remove a predicted signal peptide. This could even be used for trimming of sequencing reads (for small datasets, e.g. capillary reads). Is there anything like this in Galaxy already? If so I can't find it ;) I've also skimmed the tool shed. Regards, Peter

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Toronto GMOD meeting registration now open
by Dave Clements 13 Aug '11

13 Aug '11

Hello all, The next GMOD meeting has been schedule for this October in Toronto. See below for details. Dave C ---------- Forwarded message ---------- From: Scott Cain <scott(a)scottcain.net> Date: Fri, Aug 12, 2011 at 9:23 AM Subject: [Gmod-announce] Toronto GMOD meeting registration now open Hello, I am pleased to announce that registration is now open for the October 12-13 GMOD meeting at OICR in Toronto, Canada. Please visit the registration site at: http://gmod.eventbrite.com/ The registration fee for the meeting is $40 if registered before September 13. After September 13, the registration fee goes up to $50. For more information about the meeting, including information on our excellent keynote speakers, Gary Bader and Michael Brudno, please visit the meeting page: http://gmod.org/wiki/October_2011_GMOD_Meeting While at the meeting page, please make sure to suggest topics, talks and satellites for the meeting. I look forward to seeing you in Toronto! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------------------------------------------------------------------------- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Quota
by Steve Taylor 12 Aug '11

12 Aug '11

Hi, Are there any plans to have a disk space quota for Galaxy users that can be set by admins? Thanks, Steve

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faToTwoBit
by Peter Cock 12 Aug '11

12 Aug '11

Hi all, I recently started trying "Extract Genomic DNA" which requires faToTwoBit, which wasn't listed on the dependencies page (fixed now), http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies See also: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006366.html In updating the wiki I've assumed faToTwoBit comes from the same place as twoBitToFa, where the link given is simply: http://hgdownload.cse.ucsc.edu/admin/exe/ That just contains pre-compiled binaries - but there is no sign of the source code or a licence file. Are you just using these binaries? I feel like I've been getting lost in the UCSC website... I eventually found Jim Kent's pages, which appears to host the twoBitToFa source code along with other tools like BLAT, http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/utils/twoBitToFa/ The log files hinted at there being a git repository, which I found here, http://genome-source.cse.ucsc.edu/ http://genome.ucsc.edu/admin/git.html The licensing is murky, apparently free to use for personal, academic, and non-profit use - but no mention about potential redistribution or modification rights: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/README > ... All files are copyrighted, but license is hereby granted > for personal, academic, and non-profit use. license is > also granted for the contents of the top level lib, inc and > utils directories for commercial users. ... Have the Galaxy team made special arrangements to license faToTwoBit for use on the Penn State public server, or is this fine because faToTwoBit is under the top level utils directory? Have I overlooked some general page introducing the Kent tools like faToTwoBit? If such a page exists, could it be linked to from the Galaxy Tool Dependencies page? Thanks, Peter

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Re: [galaxy-dev] faToTwoBit (and other Kent tools like liftOver)
by Peter Cock 12 Aug '11

12 Aug '11

On Fri, Aug 12, 2011 at 11:38 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > Hi all, > > I recently started trying "Extract Genomic DNA" which requires > faToTwoBit, which wasn't listed on the dependencies page > (fixed now), http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies > > See also: > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006366.html > > In updating the wiki I've assumed faToTwoBit comes from the same > place as twoBitToFa, where the link given is simply: > http://hgdownload.cse.ucsc.edu/admin/exe/ > > That just contains pre-compiled binaries - but there is no sign > of the source code or a licence file. Are you just using these > binaries? Would I be right to guess the Penn State cluster is all 64bit Linux? Some of our cluster nodes are just 32bit, so I wanted to grab the 32bit binaries for faToTwoBit, twoBitToFa and liftOver - but this folder just contains liftOver at the moment: http://hgdownload.cse.ucsc.edu/admin/exe/linux.i386/ I guess I'll have to compile faToTwoBit and twoBitToFa from source... > .. > The licensing is murky, apparently free to use for personal, > academic, and non-profit use - but no mention about potential > redistribution or modification rights: > http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/README > >> ... All files are copyrighted, but license is hereby granted >> for personal, academic, and non-profit use. license is >> also granted for the contents of the top level lib, inc and >> utils directories for commercial users. ... > > Have the Galaxy team made special arrangements to license > faToTwoBit for use on the Penn State public server, or is this > fine because faToTwoBit is under the top level utils directory? That's fine for faToTwoBit and twoBitToFa, but... What about the liftOver tool? This is under the hg top level folder, and thus is NOT licensed for commercial users - only for personal, academic, and non-profit use. How is Galaxy able to use this tool on the public Penn State server? Regards, Peter

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Fixed: Error uploading files through filesystem paths: MacOS, Postgres and galaxy-central
by Camille Stephan 11 Aug '11

11 Aug '11

Sorry guys, didn't change file permissions for the new 'galaxy' user. Thanks anyway, Camille. -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553

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What happened to 'normal' priority on the issue tracker?
by Peter Cock 11 Aug '11

11 Aug '11

Hi all, I'm just filing a bug on bitbucket, and noticed the default priority is now major (!) We can choose: Trivial, Minor, Major, Critical, Blocker Wasn't there previously a 'Normal' which was the default? Peter

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using <validator> tags with regular expressions or mathematical expressions...
by Nikhil Joshi 10 Aug '11

10 Aug '11

Hi all, I would like to use the validator tag to validate data using either regexes or math expressions. How can I do this? I tried using the "regex" type, but I'm not sure where to put the regex itself. I tried putting it in a file that was in the filename attribute, but that didn't seem to work. Essentially, I want to check if an integer input is even or not. - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.edu

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