August 2010 - galaxy-dev - lists.galaxyproject.org

bulk datatype change
by Davide Cittaro 25 Aug '10

25 Aug '10

Hi all, bigwig and bigbed were recently added to galaxy, but it happens I had implemented those some time ago in my local instance. Fortunately your class definition is not much different from the one I've written (not even the class name). BTW, most of my bigWigs have .bw extension, whereas your implementation assumes they have .bigwig extension; .bw files are not recognized as bigWig by default (they are now "Roadmap" type) and I would like to set the proper type for all of them. Obviously, setting this one by one in the data admin window is a tedious long job... is there a way to do it automatically? It would be nice if one can select multiple datasets in admin and edit some properties (i.e. data type, database...), in addition to "edit permissions" and "delete" operations. d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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custom UCSC browser
by Davide Cittaro 25 Aug '10

25 Aug '10

Hi again, I'm afraid I've lost some configuration to get my own UCSC browser listed in the "display at" for BAM, bed, bigwig files... Can anybody post a check-list to configure this :-) ? I believe I have all pieces in their place but evidently something is wrong: this def is into ini files ucsc_display_sites = main,campus and this is in tool-data/shared/ucsc/ucsc_build_sites.txt campus http://genome.ifom-ieo-campus.it/cgi-bin/hgTracks? hg19,hg18,hg17,mm9,mm8,rn4,danRer6,danRer5,ci2,ce6,ce4,cb3,dm3,sacCer2,sacCer1 thanks! d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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galaxy-dist down?
by Leandro Hermida 24 Aug '10

24 Aug '10

Hi there, For some reason http://bitbucket.org/galaxy/galaxy-dist/ is down, i am getting a 503 Service Temporarily Unavailable, is there a planned maintenance? best, Leandro

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Apache proxy configuration
by sohkhan＠notes.cc.sunysb.edu 23 Aug '10

23 Aug '10

Hi I installed Galaxy on Mac OS 10.6.4, everything was working fine until I tried to use Apache server. I followed the directions as per http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. Added the following to my httpd.cof RewriteEngine on <Location "/"> # Define the authentication method AuthType Basic AuthName Galaxy AuthUserFile /home/nate/htpasswd Require valid-user # Define Galaxy as a valid Proxy <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> # Take the $REMOTE_USER environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e </Location> RewriteRule ^/static/style/(.*) /home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /home/nate/galaxy_dist/static/$1 [L] RewriteRule ^/favicon.ico /home/nate/galaxy_dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/nate/galaxy_dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] </Location> I am getting a "<Proxy not allowed here" error where I start apache. Any help is appreciated. -Sohail

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Galaxy Tool Shed now allows you to rate and review tools
by Greg Von Kuster 20 Aug '10

20 Aug '10

Hello Galaxy Community, The Galaxy Tool Shed at http://usegalaxy.org/community now allows you to rate and review tools contributed by others. Please keep sharing your tools - doing so provides a significant benefit to the community! Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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August 20, 2010 Galaxy Development News Brief
by Greg Von Kuster 20 Aug '10

20 Aug '10

The latest news brief is available at the following link. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Two questions: Daemon (no error code returned) and access configuration arguments
by padioleau 20 Aug '10

20 Aug '10

Dear Galaxy developers, I have two questions: First, when Galaxy is launched in daemon mode, there is no error returned if Galaxy does not start properly. For instance if the database needs to be updated, the daemon will succeed (no error code is returned) even though Galaxy is not started. I would like to know if it is possible to change that. Second, and for something completely different, I would like to know how I can get within a tool wrapper access to Galaxy configuration arguments like 'new_file_path' for example. Thanks, Ismael -- Padioleau Ismael EMBL Heidelberg ( V205)

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Re: [galaxy-dev] [galaxy-user] why is ./tools/sr_mapping/bowtie_color_wrapper.xml not implemented by default?
by Kelly Vincent 20 Aug '10

20 Aug '10

Kevin, Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup) which details how to set these up. Let us know if you need further information. (Note that this topic is better suited to galaxy-dev instead of galaxy- user since it's about local installations.) Regards, Kelly Galaxy Team On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote: > Hi, > I see that the public galaxy at usegalaxy.org > has a few differences with a local installation in that some tools > are not implemented as well. > for e.g. > ./tools/sr_mapping/bowtie_color_wrapper.xml > > May I know if there's a reason for this? > > Cheers > Kevin > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: [galaxy-dev] Dataset generation errors
by Branden Timm 19 Aug '10

19 Aug '10

Hey Ryan, Thanks for the tip, redirecting to /dev/null works but then I lose the script output that used to be visible in the history (dataset generation still works fine). Trying to redirect stderr to stdout, using 2>&1, seems to cause a parse error in my .xml configuration file. The line: <command> soap -a $singleEndedReads -D $referenceGenome -o $output -r $multipleMatchMode 2>&1 </command> Causes my tool not to show up under the tools section at all. Cheers -Branden On 8/19/2010 9:48 AM, Ry4an Brase wrote: > On Thu, Aug 19, 2010 at 09:34:40AM -0500, Branden Timm wrote: >> Hi All, >> I have been working to integrate SOAPaligner/soap2 into my Galaxy >> instance, and now have it mostly working thanks to some good advice from >> this list. However when I execute my tool, the history item for the >> resulting dataset turns red and says an error occured while running the >> job. When I look at the error message, it is simply the output of the >> soap2 tool, as follows: >> Begin Program SOAPaligner/soap2 > [snip] >> So why is Galaxy thinking there was an error generating the dataset? Do I >> have to suppress output from soap2 using a wrapper? > Galaxy will consider the job to have errored out if any text was output > to the STDERR file handle. Output to STDOUT file handle is okay and is > saved. > > See this one for more details: > > http://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-… > > If your output is correct using > > jobcommand ARGS 2>&1 > > or > > jobcommand ARGS 2>/dev/null > > should get you there. > >

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Dataset generation errors
by Branden Timm 19 Aug '10

19 Aug '10

Hi All, I have been working to integrate SOAPaligner/soap2 into my Galaxy instance, and now have it mostly working thanks to some good advice from this list. However when I execute my tool, the history item for the resulting dataset turns red and says an error occured while running the job. When I look at the error message, it is simply the output of the soap2 tool, as follows: Begin Program SOAPaligner/soap2 Thu Aug 19 09:27:43 2010 Reference: /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index Query File a: /home/galaxy/galaxy_dist/database/files/000/dataset_150.dat Output File: /home/galaxy/galaxy_dist/database/files/000/dataset_151.dat Load Index Table ... Load Index Table OK Begin Alignment ... 131072 ok 0.46 sec 262144 ok 0.43 sec 393216 ok 0.44 sec 524288 ok 0.45 sec 655360 ok 0.44 sec 702613 ok 0.19 sec Total Reads: 702613 Alignment: 672995 (95.78%) Total Elapsed Time: 5.03 - Load Index Table: 0.48 - Alignment: 4.55 SOAPaligner/soap2 End Thu Aug 19 09:27:48 2010 Additionally, the resulting dataset is a correct, and I can view it by clicking on the eye icon for that history item. I've also taken the exact command from paster.log and run it as the galaxy user, and the script does have a 0 return code. So why is Galaxy thinking there was an error generating the dataset? Do I have to suppress output from soap2 using a wrapper? Cheers -- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm(a)glbrc.wisc.edu

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