July 2012 - galaxy-dev - lists.galaxyproject.org

Build indexes for BWA, Bowtie, and others in local instance
by Di Nguyen 24 Jul '12

24 Jul '12

Dear all, I just installed my local instance. In order to use NGS tools, I need indexes. Do I have to build these indexes species by species, program by programs or there is a SHORTCUT for Galaxy compatible readied for download indexes? If I'am not mistaken, building these indexes can take weeks? Kindest regards, Di

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Local Instance is running way too slow!!!
by Di Nguyen 24 Jul '12

24 Jul '12

Dear All, I successfully install Galaxy onto my new MBP with 16Gb or Ram but when I tried to use Galaxy, it is painfully slow! The first test I did was to create Admin and import data (RNA-seq fastq, about 6Gb in size) into database and then history. The second test was to run fasqgroomer on this fasq and it took forever (a couple of hours and still running). Anybody got in idea of why it is so slow? Would it be possible that Galaxy was set up to run a single process instead of 8-core processor? If that is the case, how to fix it? Please help! Di Nguyen Postdoc, U of W, Seattle, WA

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loading bam file to galaxy
by Maya Abraham-Malaev 24 Jul '12

24 Jul '12

Hello, I'm running a local installation of galaxy. While loading a bam file (2GB) to galaxy, I get the following error: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 403, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 331, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1220, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory I've succeeded to execute other commands that used samtools. I've also succeeded in running the command: subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] in python on the server which galaxy installed on, logged in to the user under which galaxy is executed. Do you have any idea what can cause it, and how to solve the problem? Maya

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PBSpro Cluster Server possible?
by Stephan Frickenhaus 24 Jul '12

24 Jul '12

Hello, I have tried to couple our GALAXY-server (unified, running on a virtual server, ubuntu 12) with our big SGI Cluster-Server uv100 running PBSpro as job system (pbs_version = PBSPro_11.1.1.112253). On the GALAXY-server I have installed ii pbs-drmaa-dev 1.0.10-2 DRMAA for Torque/PBS Pro - devel ii pbs-drmaa1 1.0.10-2 DRMAA for Torque/PBS Pro - runtime We have the GALAXY-sources installed very recently; job-creation is prepared, but no job is scheduled to our uv100. Did you ever hear that the libdrmaa.so coming with this package is useful to couple to a PBSpro-server? The DRMAA_LIBRARY_PATH has been set accordingly to /usr/lib/libdrmaa.so.1.0.10 . we set default_cluster_job_runner = drmaa://uv100.awi.de/slong/ We also checked that the torque-system on the GALAXY-Server could successfully submit jobs by "qsub" on the PBSpro-server in the slong queue. Best regards and many thanks in advance, S. Frickenhaus -- -- Prof. Dr. Stephan Frickenhaus Hochschule Bremerhaven An der Karlstadt 8 27568 Bremerhaven 0471-4823-525 0151-1741 1631 Alfred-Wegener-Institut f. Polar- u. Meeresforschung Am Handelshafen 12 27570 Bremerhaven stephan.frickenhaus(a)awi.de 0471-4831-1179 0151-1741 1631 -- Prof. Dr. Stephan Frickenhaus FB1 - Biotechnologie Hochschule Bremerhaven An der Karlstadt 8 27568 Bremerhaven 0471-4823-525 0151-1741 1631 Alfred-Wegener-Institut f. Polar- u. Meeresforschung Bioinformatik/Rechenzentrum Am Handelshafen 12 27570 Bremerhaven stephan.frickenhaus(a)awi.de 0471-4831-1179 0151-1741 1631

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Multiple .CEL file import for microarray analysis
by Jon Manning 23 Jul '12

23 Jul '12

Hi all, My apologies if this seems obvious to many of you (seems like something that will have been dealt with)- but I've been rooting around in the docs and mailing list to no concrete avail. I'm looking to Galaxyise our existing (somewhat informal) microarray analysis workflows. I've found rexpression etc and the associated helpful datatypes. But I'm stuck at the import of .CEL files: * Do I need to create a new datatype to represent .CEL? The fact this doesn't exist by default suggests it's not the right approach. * Assuming I was to do the above, how would I create a function to generate an affyBatch (for example) from an unspecified number of input .CEL? * Is the solution to have R work with a .tar and a config file to produce the affyBatch, thereby bypassing the .CEL requirement? But then there's no .tar datatype either..... If I've missed the docs I'm happy to be chided and pushed in the right direction. Many thanks, Jon -- Dr Jonathan Manning Bioinformatics Team Centre for Cardiovascular Science University of Edinburgh Queens Medical Research Institute 47 Little France Crescent Edinburgh EH16 4TJ United Kingdom T: +44 131 242 6700 F: +44 131 242 6782 E: jmanning(a)staffmail.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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dns lookup failure and proxy errors from internal toolshed?
by Smithies, Russell 23 Jul '12

23 Jul '12

I'm trying to setup an internal toolshed but am getting DNS and proxy errors: (I'm using port 8081 instead of 9009) The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /toolshedrepository/browse_valid_repositories<http://galaxy-dev.agresearch.co.nz/toolshedrepository/browse_valid_reposito…>. Reason: DNS lookup failure for: localhost:8081repository I'm rewriting my URLs like this: RewriteRule ^/toolshed$ /toolshed/ [R] RewriteRule ^/toolshed/static/style/(.*) /var/lib/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/toolshed/static/scripts/(.*) /var/lib/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/toolshed/static/(.*) /var/lib/galaxy/static/$1 [L] RewriteRule ^/toolshed/favicon.ico /var/lib/galaxy/static/favicon.ico [L] RewriteRule ^/toolshed/robots.txt /var/lib/galaxy/static/robots.txt [L] RewriteRule ^/toolshed(.*) http://localhost:8081$1 [P] I think it might be an Apache problem but no idea hat to try next. Any ideas? Thanx, Russell Smithies Invermay Agricultural Centre Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand T +64 3 489 3809 F +64 3 489 3739 www.agresearch.co.nz<http://www.agresearch.co.nz/> ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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No action for /admin_toolshed/prepare_for_install
by Pete Schmitt 22 Jul '12

22 Jul '12

I'm trying to install deseq_and_sam2counts from the main toolshed using the admin interface in galaxy. I get the following error: The resource could not be found. No action for /admin_toolshed/prepare_for_install This is on a server that was installed in May 2012. I had performed an 'hg pull -u' on the server and restarted it to see if that would help which it didn't. I was successful installing this tool with a new install of the server on my laptop. I would prefer not to do a fresh install of this main server since it's in use. Is there a manual method to installing tools like this from the toolshed? -- * *

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Is the galaxy main toolshed compatible with local installs of galaxy-dist?
by Ira Cooke 21 Jul '12

21 Jul '12

I was wondering whether the general policy is to keep the toolshed at toolshed.g2.bx.psu.edu compatible with galaxy-dist or galaxy-central. The reason I ask is that I went to install a tool from a production server I'm trying to setup based on galaxy-dist ... but got an error; The resource could not be found. No action for /admin_toolshed/prepare_for_install Searching for this in the source code, I found that it exists in galaxy-central ... but not in galaxy-dist Am I right in guessing that this error is due to toolshed.g2.bx.psu.edu being powered by a recent toolshed version that is incompatible with galaxy-dist? If so, it would be great to get clarification as to whether this is to be expected in future. My personal feeling is that the main toolshed would be much more useful if kept compatible with galaxy-dist. Cheers Ira

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Lost my data on Galaxy
by GEISER Céline 21 Jul '12

21 Jul '12

Hi, When I started Galaxy today I lost more than half of my processed data, weeks of work ;-(. I had a look at the deleted dataset but nothing, If I had erased them erroneously I wouldn't have purge them.... Is it possible that there was a problem with the server? Or do a kind of logfile/history exist to see everything what happened on the account? Thanx and have a nice week-end Céline

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Galaxy July 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Jul '12

21 Jul '12

Galaxy July 20, 2012 Distribution & News Brief *Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20* *Highlights: http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief* * *Freebayes *has moved from the /Galaxy distribution to the Galaxy's Main Tool Shed/ * *EMBOSS* version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing. * *Tool Shed* now also supports specifying the third party tool dependencies to be automatically installed in new repositories * *Admin Genome Indexing* is now in /BETA/. Download, index, and track progress right from the admin UI! * *Improved Error Handling* that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details. * *TopHat2/Bowtie2* latest support includes option to 'report discordant pairs', updated tests, and more preset options. * *Trackster* new parameter space visualization. /Includes BRAND NEW Features!!/ More details coming soon, but give a test drive now. *http://getgalaxy.org* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ec29ce8e27a1 *Thanks for using Galaxy!* We hope to see everyone in /Chicago/ @ *GCC2012*!! The Galaxy Team

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