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

displaying data in Gbrowse
by Nicki Gray 13 Dec '10

13 Dec '10

Hi, I have been trying to send data to our Gbrowse2 servers from within Galaxy. I found some information from Greg Von Kuster (below) explaining how to change the configuration settings. I edited ~/universe_wsgi.ini and ~/tool-data/shared/gbrowse/ gbrowse_build_sites.txt We have python 2.6 and the file ~/lib/galaxy/datatypes/interval.py has the following in the class Gff section: self.add_display_app( 'gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) but I still only see "display at UCSC" - there is no "display at GBrowse" link Is there another file I need to edit in order to get this link to show as an option? Thanks, Nicki --------------------- Nicki Gray MRC Molecular Haematology Unit 01865 222434 >> > On Mon, Mar 15, 2010 at 10:46 AM, Jelle Scholtalbers < >> > j.scholtalbers at gmail.com> wrote: >> > >> >> Hi Greg, >> >> >> >> thank you for the explanation, could this also be included >> somewhere in >> >> the wiki? >> >> Although I do get far I don't get the tracks to display in my >> GBrowse. The >> >> link does redirect me to the appropriate gbrowse that I >> specified, the >> >> uploaded track is displayed as: >> >> "could not fetch data for >> >> http://galaxyserver/galaxy/root/display_as?id=4047&display_app=c_elegans&au… >> " >> >> with the label "galaxyserver/display_as". >> >> When I then follow that link I actually see the data as GFF, but >> it seems >> >> GBrowse can't retrieve it somehow. >> >> >> >> This was tested under: >> >> Galaxy-central - 3528:48e83411aa91 >> >> and GBrowse 1.995 >> >> >> >> Two other things: >> >> - under python 2.6 the links appear, under 2.4 they don't. >> >> - The links are displayed as "display in wormbase" and the >> >> display_app="c_elegans". This seems to be harcoded at >> >> galaxy.datatypes.interval line 572, would be nice to have that >> dynamically >> >> generated from for example the >> >> ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt >> >> >> >> Cheers, >> >> Jelle >> >> >> >> >> >> On Fri, Mar 12, 2010 at 3:25 PM, Greg Von Kuster <greg at >> bx.psu.edu> wrote: >> >> >> >>> This requires only configuration settings, not an actual tool >> like >> >>> Epigraph. Displaying in GBrowse is done the same way as >> displaying in UCSC. >> >>> >> >>> In you universe_wsgi.ini file, look for hte following setting, >> and set >> >>> your GBrowse accordingly - you may only want 1 site instead of >> the 3 in the >> >>> sample. >> >>> >> >>> # Comma separated list of bx / UCSC / gbrowse / GeneTrack >> browsers to use >> >>> for viewing >> >>> bx_display_sites = main >> >>> ucsc_display_sites = main,test,archaea,ucla >> >>> gbrowse_display_sites = main,test,tair >> >>> >> >>> Next, make the setting in >> >>> ~/tool-data/shared/gbrowse/gbrowse_build_sites.txt - here are >> the sample >> >>> settings ( note that each corresponds to what you configured in >> your >> >>> universe_wsgi.ini file ). White spaces are tabs in this file, >> and the first >> >>> value in each line ( e.g., main, test ) is the link label that >> points to the >> >>> GBrowse site whose URL is in the 2nd column. The 3rd column of >> each line is >> >>> the valid builds for which the link will be displayed ( see >> below ). Note >> >>> that the sample builds are no longer valid, they should be >> value slike ce2, >> >>> ce3, etc - see ~/tool-data/shared/ucsc/builds.txt for valid >> values ). >> >>> >> >>> # wormbase sites / supported genomes >> >>> main http://www.wormbase.org/db/seq/gbgff/c_elegans/ >> >>> >> c_elegans >> ,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi >> >>> test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ >> >>> >> c_elegans >> ,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi >> >>> tair http://arabidopsis.org/cgi-bin/gbrowse/ >> >>> arabidopsis_tair8,arabidopsis >> >>> >> >>> When you have the correct configuration settings, you'll see a >> link in >> >>> history items ( here is an example - display in Wormbase main ) >> whose genome >> >>> build matches one of the configured builds.

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Warning message display on the main galaxy website
by Assaf Gordon 13 Dec '10

13 Dec '10

Hi, On the main website there's a yellow warning message about the cooling hardware failure - it's very nice (not the failure, the message display). Is there a standard way to add those on a local instance (through the "admin" pages, perhaps) ? or did you just temporarily changed "base_panels.mako" ? Thanks, -gordon

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galaxy lims issues
by nsfox＠uwaterloo.ca 10 Dec '10

10 Dec '10

Hi, I'm having a few issues with the galaxy lims system. First, when I try to upload a dataset with the Upload files from filesystem paths option, I'm getting the following error: Traceback (most recent call last): File "/share/galaxy/tools/data_source/upload.py", line 414, in ? __main__() File "/share/galaxy/tools/data_source/upload.py", line 389, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File "/share/ error Any ideas as to what might be wrong would be great! Also, I think the following might be bugs. 1. I can log out twice and then I have to log in twice. When I log out, galaxy goes to the analyze data tab rather than the login page but it does say that I am logged out. The user tab however says that I am logged in and gives me the option to log out again. If I refresh the page it acts like I'm logged out and redirects to the login page. 2. In the lims system, the order of the fields in the grid level for when entering the information about a sample changes from the order in the sample sequencing form. Lastly I was wondering if it was changed on purpose so that a non-admin user can change the information about a sample once the sequencing request is submitted. It used to be that a regular user could not edit data after they had submitted the sequencing request. Thanks so much, Natalie

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[patch] remote user custom genomes
by Ry4an Brase 10 Dec '10

10 Dec '10

We use external authentication for our Galaxy setup and custom reference genomes weren't working until JJ made this small patch: https://bitbucket.org/Ry4an/galaxy-umn-msi-changes/src/1d3e4c47468e/remote-… Please consider it for addition to galaxy-central. Thanks, -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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Re: [galaxy-dev] invoking galaxy standalone
by Kelly Vincent 10 Dec '10

10 Dec '10

Hi Sean, It's pretty standard that if you close a terminal window with a process running in it, that process doesn't necessarily shut down properly, though after a while it will clean itself up. Shutting the browser or not will have absolutely no impact. So you can either leave open the terminal window with Galaxy running, or stop the server before exiting the terminal window. Alternatively, you can also run Galaxy as a background process if you don't want to bother with leaving the terminal window open ("sh run.sh --daemon" to start it and "sh run.sh --stop-daemon" to stop it). Just bear in mind that if you run it as a background process, you won't see any error messages unless you inspect the paster log. As far as which port number to use, 8080 is a very common default, but anything higher than that is a good bet. It's usually good to just choose an arbitrary "odd" number (8976 rather than 9000, for instance). There's always a small chance you'll run into a conflict with another program, so if you ever see an error referencing a port number, just try changing Galaxy's. For moving it to another directory, I think that should be okay. You may need to rerun setup.sh. Regards, Kelly On Dec 10, 2010, at 9:50 AM, Sean Rogers wrote: > I shut quit the terminal and safari which were both running from > yesterday. Galaxy opened through the new terminal command using the > default port. This is semi-inconvenient. Any suggestions as to which > port number to change to? Do I pull a number from a hat or are there > only certain numbered ports available? > > I installed galaxy in my home directory. Can I move it to /usr/ > local/ with the mv command and still have everything work? > > Thanks again,Sean > > > > > Quoting Kelly Vincent <kpvincent(a)bx.psu.edu>: > > > Sean, > > > > This message means that the port specified in universe_wsgi.ini is > > being used by something else (or possibly Galaxy if you never > stopped > > the server you started yesterday). You should probably change port > > from the default 8080 if you haven't already. Let us know if you > have > > any further questions. > > > > Regards, > > Kelly > > > > > > > > On Dec 10, 2010, at 9:01 AM, Sean Rogers wrote: > > > >> Hello, > >> > >> I downloaded and set up galaxy yesterday. It opened up the local > >> host fine at that time. I went to reopen galaxy today by using > >> run.sh from the command line. Galaxy did not open and I got the > >> message: > >> > >> File > >> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/ > SocketServer.py", line 413, in > >> server_bind > >> > >> self.socket.bind(self.server_address) > >> > >> File "<string>", line 1, in bind > >> > >> socket.error: [Errno 48] Address already in use > >> > >> > >> > >> > >> > >> Sean A. Rogers > >> > >> ************************************** > >> Visiting Research Associate > >> Department of Horticulture > >> A314 - Plant & Soil Sciences Building > >> Michigan State University > >> East Lansing, MI 48824-1325 > >> > >> Phone: (517) 355-5191 x1373 > >> > **************************************_______________________________________________ > >> galaxy-dev mailing list > >> galaxy-dev(a)lists.bx.psu.edu > >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > > > Sean A. Rogers > > ************************************** > Visiting Research Associate > Department of Horticulture > A314 - Plant & Soil Sciences Building > Michigan State University > East Lansing, MI 48824-1325 > > Phone: (517) 355-5191 x1373 > **************************************

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invoking galaxy standalone
by Sean Rogers 10 Dec '10

10 Dec '10

Hello, I downloaded and set up galaxy yesterday. It opened up the local host fine at that time. I went to reopen galaxy today by using run.sh from the command line. Galaxy did not open and I got the message: File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 48] Address already in use Sean A. Rogers ************************************** Visiting Research Associate Department of Horticulture A314 - Plant & Soil Sciences Building Michigan State University East Lansing, MI 48824-1325 Phone: (517) 355-5191 x1373 **************************************

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Installing Galaxy on SGE cluster
by Zachariah Z 09 Dec '10

09 Dec '10

Hello gurus, This is my first attempt at installing Galaxy on a Solaris10 x86 platform with SGE 6.2 cluster that I had set up. I am using the unified method on an NFS mounted directory called /gtools. I first proceeded to download and install Python 2.6.6 onto /gtools. After this, I proceeded to download the latest source of galaxy using mercurial check out. I set the following environment variables: DRMAA_LIBRARY_PATH=/share/sgeroot/lib/sol-amd64/lbdrmaa.so.1.0 TEMP=/gtools/galaxy/galaxy-dist/database/tmp Upon running the startup script run.sh I get the error : Exception: DRMAAJobRunner requires drmaa module which could not be loaded: No module named _ctypes. The following is the transcript, I appreciate any help in resolving this Thanks in advance --Zac sh run.sh python path is: /gtools/galaxy/galaxy-dist/eggs/numpy-1.3.0-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/pysam-0.1.1_kanwei_90e03180969d-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Beaker-1.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/docutils-0.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /gtools/galaxy/galaxy-dist/lib, /gtools/src/galaxy_env/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg, /gtools/src/galaxy_env/lib/python2.6/site-packages/pip-0.8.2-py2.6.egg, /gtools/src/galaxy_env/lib/python26.zip, /gtools/src/galaxy_env/lib/python2.6, /gtools/src/galaxy_env/lib/python2.6/plat-sunos5, /gtools/src/galaxy_env/lib/python2.6/lib-tk, /gtools/src/galaxy_env/lib/python2.6/lib-old, /gtools/src/galaxy_env/lib/python2.6/lib-dynload, /gtools/python/current/lib/python2.6, /gtools/python/current/lib/python2.6/plat-sunos5, /gtools/python/current/lib/python2.6/lib-tk, /gtools/src/galaxy_env/lib/python2.6/site-packages galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,330 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,339 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,345 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,347 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,354 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,360 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,378 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,380 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,392 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,397 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,403 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False galaxy.datatypes.assembly DEBUG 2010-12-08 17:19:21,406 Velvet log info JJ __init__ galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,421 Loaded sniffer for datatype: galaxy.datatypes.binary:Bam galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.binary:Sff galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.xml:BlastXml galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.sequence:Maf galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.sequence:Lav galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.sequence:csFasta galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScore454 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fasta galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fastq galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.interval:Wiggle galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.images:Html galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.images:Pdf galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.sequence:Axt galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.interval:Bed galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.interval:CustomTrack galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff3 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.tabular:Pileup galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,426 Loaded sniffer for datatype: galaxy.datatypes.interval:Interval galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,426 Loaded sniffer for datatype: galaxy.datatypes.tabular:Sam galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,426 Loaded sniffer for datatype: galaxy.datatypes.tabular:Vcf galaxy.model.migrate.check DEBUG 2010-12-08 17:19:21,538 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.model.migrate.check INFO 2010-12-08 17:19:21,622 At database version 62 galaxy.model.custom_types DEBUG 2010-12-08 17:19:21,630 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tools.data DEBUG 2010-12-08 17:19:21,636 Loaded tool data table 'all_fasta galaxy.tools.data DEBUG 2010-12-08 17:19:21,637 Loaded tool data table 'bfast_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,638 Loaded tool data table 'blastdb galaxy.tools.data DEBUG 2010-12-08 17:19:21,638 Loaded tool data table 'blastdb_p galaxy.tools.data DEBUG 2010-12-08 17:19:21,639 Loaded tool data table 'bowtie_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,640 Loaded tool data table 'bowtie_indexes_color galaxy.tools.data DEBUG 2010-12-08 17:19:21,641 Loaded tool data table 'bwa_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,642 Loaded tool data table 'indexed_maf_files galaxy.tools.data DEBUG 2010-12-08 17:19:21,642 Loaded tool data table 'ngs_sim_fasta galaxy.tools.data DEBUG 2010-12-08 17:19:21,643 Loaded tool data table 'lastz_seqs galaxy.tools.data DEBUG 2010-12-08 17:19:21,644 Loaded tool data table 'perm_base_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,644 Loaded tool data table 'perm_color_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,645 Loaded tool data table 'srma_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,645 Loaded tool data table 'tophat_indexes galaxy.tools INFO 2010-12-08 17:19:21,645 parsing the tool configuration galaxy.tools DEBUG 2010-12-08 17:19:21,660 Loading section: Get Data galaxy.tools DEBUG 2010-12-08 17:19:21,997 Loaded tool: upload1 1.1.2 galaxy.tools DEBUG 2010-12-08 17:19:22,002 Loaded tool: ucsc_table_direct1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,007 Loaded tool: ucsc_table_direct_test1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,011 Loaded tool: ucsc_table_direct_archaea1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,015 Loaded tool: bx_browser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,095 Loaded tool: microbial_import1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,099 Loaded tool: biomart 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,103 Loaded tool: biomart_test 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,107 Loaded tool: cbi_rice_mart 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,111 Loaded tool: gramenemart 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,114 Loaded tool: modENCODEfly 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,117 Loaded tool: flymine 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,121 Loaded tool: flymine_test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,123 Loaded tool: modmine 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,126 Loaded tool: ratmine 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,130 Loaded tool: modENCODEworm 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,134 Loaded tool: wormbase 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,137 Loaded tool: wormbase_test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,140 Loaded tool: eupathdb 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,143 Loaded tool: encode_db1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,146 Loaded tool: epigraph_import 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,150 Loaded tool: epigraph_import_test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,155 Loaded tool: hbvar 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,167 Loaded tool: fix_errors 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,168 Loading section: Send Data galaxy.tools DEBUG 2010-12-08 17:19:22,199 Loaded tool: epigraph_export 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,234 Loaded tool: epigraph_test_export 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,234 Loading section: ENCODE Tools galaxy.tools DEBUG 2010-12-08 17:19:22,293 Loaded tool: gencode_partition1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,349 Loaded tool: random_intervals1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,349 Loading section: Lift-Over galaxy.tools DEBUG 2010-12-08 17:19:22,381 Loaded tool: liftOver1 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:22,382 Loading section: Text Manipulation galaxy.tools DEBUG 2010-12-08 17:19:22,412 Loaded tool: addValue 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,456 Loaded tool: Add_a_column1 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:22,481 Loaded tool: cat1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,541 Loaded tool: Cut1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,569 Loaded tool: mergeCols1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,597 Loaded tool: Convert characters1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,620 Loaded tool: createInterval 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,683 Loaded tool: Cut1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,722 Loaded tool: ChangeCase 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,746 Loaded tool: Paste1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,763 Loaded tool: Remove beginning1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,781 Loaded tool: random_lines1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,799 Loaded tool: Show beginning1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,826 Loaded tool: Show tail1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,875 Loaded tool: trimmer 0.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,970 Loaded tool: dna_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,024 Loaded tool: tables_arithmetic_operations 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,025 Loading section: Filter and Sort galaxy.tools DEBUG 2010-12-08 17:19:23,111 Loaded tool: Filter1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,149 Loaded tool: sort1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,379 Loaded tool: Grep1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,406 Loaded tool: Extract_features1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,453 Loaded tool: gff_filter_by_attribute 0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,472 Loaded tool: gff_filter_by_feature_count 0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,472 Loading section: Join, Subtract and Group galaxy.tools DEBUG 2010-12-08 17:19:23,521 Loaded tool: join1 2.0.2 galaxy.tools DEBUG 2010-12-08 17:19:23,550 Loaded tool: comp1 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:23,607 Loaded tool: subtract_query1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,656 Loaded tool: Grouping1 1.9.1 galaxy.tools DEBUG 2010-12-08 17:19:23,688 Loaded tool: column_join 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:23,688 Loading section: Convert Formats galaxy.tools DEBUG 2010-12-08 17:19:23,753 Loaded tool: axt_to_concat_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,814 Loaded tool: axt_to_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,891 Loaded tool: axt_to_lav_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,920 Loaded tool: bed2gff1 2.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,941 Loaded tool: fasta2tab 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,971 Loaded tool: gff2bed1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,014 Loaded tool: lav_to_bed1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,132 Loaded tool: MAF_To_BED1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,227 Loaded tool: MAF_To_Interval1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,345 Loaded tool: MAF_To_Fasta1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,367 Loaded tool: tab2fasta 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:24,382 Loaded tool: fastq_to_fasta_python 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,434 Loaded tool: wiggle2simple1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,450 Loaded tool: Sff_extractor 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,500 Loaded tool: gtf2bedgraph 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,540 Loaded tool: wig_to_bigWig 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,540 Loading section: Extract Features galaxy.tools DEBUG 2010-12-08 17:19:24,571 Loaded tool: gene2exon1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,572 Loading section: Fetch Sequences galaxy.tools DEBUG 2010-12-08 17:19:24,637 Loaded tool: Extract genomic DNA 1 2.2.1 galaxy.tools DEBUG 2010-12-08 17:19:24,637 Loading section: Fetch Alignments galaxy.tools DEBUG 2010-12-08 17:19:24,679 Loaded tool: Interval2Maf_pairwise1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,709 Loaded tool: Interval2Maf1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,789 Loaded tool: MAF_split_blocks_by_species1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,833 Loaded tool: Interval_Maf_Merged_Fasta2 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,879 Loaded tool: GeneBed_Maf_Fasta2 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,962 Loaded tool: maf_stats1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,980 Loaded tool: MAF_Thread_For_Species1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,012 Loaded tool: MAF_Limit_To_Species1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,027 Loaded tool: maf_limit_size1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,043 Loaded tool: maf_by_block_number1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,061 Loaded tool: MAF_Reverse_Complement_1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,112 Loaded tool: MAF_filter 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,112 Loading section: Get Genomic Scores galaxy.tools DEBUG 2010-12-08 17:19:25,161 Loaded tool: wiggle2simple1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,317 Loaded tool: aggregate_scores_in_intervals2 1.1.2 galaxy.tools DEBUG 2010-12-08 17:19:25,371 Loaded tool: phastOdds_for_intervals 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,371 Loading section: Operate on Genomic Intervals galaxy.tools DEBUG 2010-12-08 17:19:25,422 Loaded tool: gops_intersect_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,576 Loaded tool: gops_subtract_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,606 Loaded tool: gops_merge_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,643 Loaded tool: gops_concat_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,669 Loaded tool: gops_basecoverage_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,710 Loaded tool: gops_coverage_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,750 Loaded tool: gops_complement_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,806 Loaded tool: gops_cluster_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,884 Loaded tool: gops_join_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,936 Loaded tool: get_flanks1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,972 Loaded tool: flanking_features_1 4.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,051 Loaded tool: Annotation_Profiler_0 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,052 Loading section: Statistics galaxy.tools DEBUG 2010-12-08 17:19:26,130 Loaded tool: Summary_Statistics1 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:26,179 Loaded tool: Count1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,253 Loaded tool: cor2 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,295 Loaded tool: generate_matrix_for_pca_and_lda1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,334 Loaded tool: lda_analy1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:26,348 Loaded tool: plot_for_lda_output1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:26,395 Loaded tool: t_test_two_samples 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,491 Loaded tool: compute_q_values 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,491 Loading section: Wavelet Analysis galaxy.tools DEBUG 2010-12-08 17:19:26,539 Loaded tool: compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,588 Loaded tool: compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,639 Loaded tool: compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,702 Loaded tool: compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,703 Loading section: Graph/Display Data galaxy.tools DEBUG 2010-12-08 17:19:26,771 Loaded tool: histogram_rpy 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:26,820 Loaded tool: scatterplot_rpy 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,846 Loaded tool: barchart_gnuplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,892 Loaded tool: XY_Plot_1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:26,910 Loaded tool: qual_stats_boxplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,948 Loaded tool: gmaj_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,974 Loaded tool: laj_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,000 Loaded tool: build_ucsc_custom_track_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,024 Loaded tool: vcf_to_maf_customtrack1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,056 Loaded tool: mutation_visualize 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,056 Loading section: Regional Variation galaxy.tools DEBUG 2010-12-08 17:19:27,111 Loaded tool: winSplitter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,171 Loaded tool: featureCoverage1 2.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,211 Loaded tool: qualityFilter 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:27,242 Loaded tool: cpgFilter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,280 Loaded tool: getIndels_2way 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,304 Loaded tool: indels_3way 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:27,327 Loaded tool: indelRates_3way 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,349 Loaded tool: substitutions1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,386 Loaded tool: subRate1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,423 Loaded tool: microsats_align1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,452 Loaded tool: microsats_mutability1 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:27,497 Loaded tool: delete_overlapping_indels 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,598 Loaded tool: compute_motifs_frequency 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,769 Loaded tool: compute_motif_frequencies_for_all_motifs 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,806 Loaded tool: categorize_elements_satisfying_criteria 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,841 Loaded tool: draw_stacked_barplots 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,841 Loading section: Multiple regression galaxy.tools DEBUG 2010-12-08 17:19:27,901 Loaded tool: LinearRegression1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:27,968 Loaded tool: BestSubsetsRegression1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,024 Loaded tool: rcve1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,024 Loading section: Multivariate Analysis galaxy.tools DEBUG 2010-12-08 17:19:28,079 Loaded tool: pca1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:28,150 Loaded tool: cca1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,185 Loaded tool: kpca1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,219 Loaded tool: kcca1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,219 Loading section: Evolution galaxy.tools DEBUG 2010-12-08 17:19:28,241 Loaded tool: hyphy_branch_lengths_wrapper1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,259 Loaded tool: hyphy_nj_tree_wrapper1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,289 Loaded tool: hyphy_dnds_wrapper1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,354 Loaded tool: mutate_snp_codon_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,405 Loaded tool: hgv_codingSnps 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,448 Loaded tool: hgv_add_scores 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,448 Loading section: Metagenomic analyses galaxy.tools DEBUG 2010-12-08 17:19:28,489 Loaded tool: Fetch Taxonomic Ranks 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:28,515 Loaded tool: t2t_report 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,594 Loaded tool: Draw_phylogram 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,649 Loaded tool: find_diag_hits 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,688 Loaded tool: lca1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:28,767 Loaded tool: poisson2test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,767 Loading section: FASTA manipulation galaxy.tools DEBUG 2010-12-08 17:19:28,787 Loaded tool: fasta_compute_length 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,815 Loaded tool: fasta_filter_by_length 1.1 galaxy.tools DEBUG 2010-12-08 17:19:28,839 Loaded tool: fasta_concatenate0 0.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,859 Loaded tool: fasta2tab 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,879 Loaded tool: tab2fasta 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:28,902 Loaded tool: cshl_fasta_formatter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,922 Loaded tool: cshl_fasta_nucleotides_changer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,945 Loaded tool: cshl_fastx_collapser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,945 Loading section: NGS: QC and manipulation galaxy.tools DEBUG 2010-12-08 17:19:28,998 Loaded tool: fastq_groomer 1.0.3 galaxy.tools DEBUG 2010-12-08 17:19:29,019 Loaded tool: fastq_paired_end_splitter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,041 Loaded tool: fastq_paired_end_joiner 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,138 Loaded tool: fastq_stats 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,188 Loaded tool: quality_score_distribution 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:29,220 Loaded tool: trim_reads 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,240 Loaded tool: fastq_combiner 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:29,280 Loaded tool: solid2fastq 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,354 Loaded tool: solid_qual_stats 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,400 Loaded tool: solid_qual_boxplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,482 Loaded tool: fastq_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,510 Loaded tool: fastq_trimmer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,537 Loaded tool: fastq_quality_trimmer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,554 Loaded tool: fastq_masker_by_quality 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,633 Loaded tool: fastq_manipulation 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:29,647 Loaded tool: fastq_to_fasta_python 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,663 Loaded tool: fastq_to_tabular 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,679 Loaded tool: tabular_to_fastq 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,710 Loaded tool: cshl_fastq_quality_converter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,805 Loaded tool: cshl_fastx_quality_statistics 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,856 Loaded tool: cshl_fastq_quality_boxplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,899 Loaded tool: cshl_fastx_nucleotides_distribution 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,927 Loaded tool: cshl_fastq_to_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,967 Loaded tool: cshl_fastq_quality_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,999 Loaded tool: cshl_fastq_to_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,137 Loaded tool: cshl_fastx_artifacts_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,163 Loaded tool: cshl_fastx_barcode_splitter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,199 Loaded tool: cshl_fastx_clipper 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:30,222 Loaded tool: cshl_fastx_collapser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,253 Loaded tool: cshl_fastx_renamer 0.0.11 galaxy.tools DEBUG 2010-12-08 17:19:30,278 Loaded tool: cshl_fastx_reverse_complement 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,312 Loaded tool: cshl_fastx_trimmer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,312 Loading section: NCBI BLAST+ galaxy.tools DEBUG 2010-12-08 17:19:30,387 Loaded tool: ncbi_blastn_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,464 Loaded tool: ncbi_blastp_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,544 Loaded tool: ncbi_blastx_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,620 Loaded tool: ncbi_tblastn_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,699 Loaded tool: ncbi_tblastx_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,756 Loaded tool: blastxml_to_tabular 0.0.1 galaxy.tools DEBUG 2010-12-08 17:19:30,757 Loading section: NGS: Mapping galaxy.tools DEBUG 2010-12-08 17:19:30,829 Loaded tool: lastz_wrapper_2 1.2.0 galaxy.tools DEBUG 2010-12-08 17:19:30,870 Loaded tool: lastz_paired_reads_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:30,967 Loaded tool: bowtie_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,070 Loaded tool: bowtie_color_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,130 Loaded tool: bwa_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,198 Loaded tool: bfast_wrapper 0.1.2 galaxy.tools DEBUG 2010-12-08 17:19:31,271 Loaded tool: megablast_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,294 Loaded tool: megablast_xml_parser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,362 Loaded tool: PerM 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,407 Loaded tool: srma_wrapper 0.2.0 galaxy.tools DEBUG 2010-12-08 17:19:31,407 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2010-12-08 17:19:31,436 Loaded tool: sam_indel_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,462 Loaded tool: indel_sam2interval 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,487 Loaded tool: indel_table 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,520 Loaded tool: indel_analysis 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,520 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2010-12-08 17:19:31,619 Loaded tool: tophat 1.2.0 galaxy.tools DEBUG 2010-12-08 17:19:31,683 Loaded tool: cufflinks 0.9.1 galaxy.tools DEBUG 2010-12-08 17:19:31,747 Loaded tool: cuffcompare 0.9.1 galaxy.tools DEBUG 2010-12-08 17:19:31,833 Loaded tool: cuffdiff 0.9.1 galaxy.tools DEBUG 2010-12-08 17:19:31,851 Loaded tool: filter_combined_via_tracking 0.1 galaxy.tools DEBUG 2010-12-08 17:19:31,851 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2010-12-08 17:19:31,892 Loaded tool: sam_bw_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,921 Loaded tool: sam2interval 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:31,941 Loaded tool: sam_to_bam 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,959 Loaded tool: bam_to_sam 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,978 Loaded tool: sam_merge 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:32,022 Loaded tool: sam_pileup 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:32,175 Loaded tool: pileup_parser 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:32,217 Loaded tool: pileup_interval 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,218 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2010-12-08 17:19:32,248 Loaded tool: peakcalling_macs 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,273 Loaded tool: bed2genetrack 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:32,304 Loaded tool: predict2genetrack 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,304 Loading section: NGS: Simulation galaxy.tools DEBUG 2010-12-08 17:19:32,336 Loaded tool: ngs_simulation 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,337 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2010-12-08 17:19:32,500 Loaded tool: upload1 1.1.2 galaxy.tools DEBUG 2010-12-08 17:19:32,502 Loaded tool: library_access1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,707 Loaded tool: rgClean1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,774 Loaded tool: rgPedSub1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,865 Loaded tool: rgLDIndep1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,911 Loaded tool: fakePhe1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,941 Loaded tool: rgfakePed1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,941 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2010-12-08 17:19:32,989 Loaded tool: rgQC1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,047 Loaded tool: rgEigPCA1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,101 Loaded tool: rgHaploView1 0.3 galaxy.tools DEBUG 2010-12-08 17:19:33,167 Loaded tool: rgManQQ1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:33,215 Loaded tool: rgGRR1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,215 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2010-12-08 17:19:33,276 Loaded tool: rgCaCo1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,329 Loaded tool: rgTDT1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,414 Loaded tool: rgGLM1 0.2 galaxy.tools DEBUG 2010-12-08 17:19:33,479 Loaded tool: rgManQQ1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:33,479 Loading section: Human Genome Variation galaxy.tools DEBUG 2010-12-08 17:19:33,535 Loaded tool: hgv_codingSnps 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,583 Loaded tool: hgv_add_scores 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,634 Loaded tool: hgv_sift 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,662 Loaded tool: hgv_linkToGProfile 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,698 Loaded tool: hgv_david 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,784 Loaded tool: hgv_ctdBatch 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,816 Loaded tool: hgv_funDo 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,857 Loaded tool: hgv_snpFreq 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,897 Loaded tool: hgv_ldtools 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,948 Loaded tool: hgv_pass 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,015 Loaded tool: hgv_gpass 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,070 Loaded tool: hgv_beam 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,142 Loaded tool: hgv_lps 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,184 Loaded tool: hgv_hilbertvis 1.0.0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,603 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,615 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,627 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,639 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,651 Loaded converter: CONVERTER_bed_to_interval_index_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,663 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,674 Loaded converter: CONVERTER_BedGraph_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,686 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,698 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,710 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,723 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,735 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,747 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,766 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,778 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,789 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,802 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,814 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,826 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,839 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,851 Loaded converter: CONVERTER_vcf_to_interval_index_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,862 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,874 Loaded converter: CONVERTER_Wiggle_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,876 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,888 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,899 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,911 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,923 Loaded converter: pbed2ldindepconvert galaxy.tools.imp_exp DEBUG 2010-12-08 17:19:36,928 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2010-12-08 17:19:36,930 Loaded history import tool: __IMPORT_HISTORY__ galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,934 Loaded external metadata tool: __SET_METADATA__ galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,952 Loaded indexer: INDEXER_Coverage_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,963 Loaded indexer: INDEXER_Coverage_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,974 Loaded indexer: INDEXER_Interval_0 galaxy.jobs.runners.local INFO 2010-12-08 17:19:36,984 starting workers galaxy.jobs.runners.local DEBUG 2010-12-08 17:19:36,986 5 workers ready Traceback (most recent call last): File "/gtools/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/app.py", line 79, in __init__ self.job_manager = jobs.JobManager( self ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 41, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1005, in __init__ self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 72, in __init__ raise Exception( "DRMAAJobRunner requires drmaa module which could not be loaded: %s" % drmaa ) Exception: DRMAAJobRunner requires drmaa module which could not be loaded: No module named _ctypes

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NGINX configuration for Galaxy production
by Richard Bruskiewich 08 Dec '10

08 Dec '10

Colleagues, I encountered a curious problem while configuring nginx as a proxy for Galaxy. I posed the question through Enis who forwarded it to one of the lists. I just want to share a solution to the issue, which could perhaps be documented in a small change to the http://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxydocumentat… page. The observed problem was that Galaxy proxied through NGINX would only display properly in Microsoft IE but not in Firefox or Opera. One of my colleagues noticed that a Firefox error console reported that the various cascading style sheets were observed as having MIME type "text/plain" not "text/css" hence, where not loaded by Firefox. Presumably IE assumed CSS file type by the context of retrieval but the other browsers were more strict. Anyhow, this suggested that although NGINX has a configuration file of MIME types associated with file extensions, the content-type wasn't being properly set. I don't know if this represents a bug in NGINX operations, but after perusing the NGINX wiki docs, I came across a directive that appeared to solve the problem: default_type. The "default_type" covers any files in a specified context (http, server, location) which don't otherwise have their MIME type recognized (for whatever reason) and is itself originally set "by default" to "text/plain", which may explain the observed error in content type sent back. What I therefore did is reset the default type, in the style sheet nginx "location" directive context, to "text/css". This appeared to work. In the nginxProxy wiki documentation page on BitBucket, somebody with editorial privileges to this page may wish to document this throughout the page where the style directives are documented , i.e. location /static/style { alias /home/nate/galaxy_dist/static/june_2007_style/blue; default_type text/css; # other directives... } Cheers, Richard Bruskiewich, PhD Senior Scientist, Computational and Systems Biology Applications Team for Computational Genomics T.T. Chang Genetic Resources Center International Rice Research Institute

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syntax error in tophat wrapper after updating
by Glen Beane 08 Dec '10

08 Dec '10

Last week we pulled the changes from galaxy-dist (our copy was a couple months old). Now when we run tophat we get a Python syntax error: An error occurred running this job:File "/<galaxy_home>/tools/ngs_rna/tophat_wrapper.py", line 196 finally: ^ SyntaxError: invalid syntax We have no local changes to the wrapper. Has this been fixed in galaxy-central? -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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statistics -> cor failing on R's is.atomic() check
by Ry4an Brase 08 Dec '10

08 Dec '10

Trying to run the unmodified cor.py tool from a current galaxy-dist we're getting this output using the sample input data: % python /project/dbw-galaxy/DEVELOPMENT/tools/stats/cor.py /project/dbw-galaxy/DEVELOPMENT/test-data/cor.tabular /tmp/cor.out.ry4an 2,3 pearson Error: is.atomic(x) is not TRUE which is happening in galaxy too. The line it's triggering is: 71 # Run correlation 72 try: 73 value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method ) 74 except Exception, exc: 75 out.close() 76 stop_err("%s" %str( exc )) and tracing through the execution the inputs look fine: Breakpoint 1 at /home/msi/ry4an/cor.py:73 (Pdb) run Restarting ./cor.py with arguments: /project/dbw-galaxy/DEVELOPMENT/test-data/cor.tabular /tmp/cor.out.ry4an465 2,3 pearson > /home/msi/ry4an/cor.py(6)<module>() -> """ (Pdb) c > /home/msi/ry4an/cor.py(73)main() -> value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method ) (Pdb) p matrix [[68.0, 4.0999999999999996], [71.0, 4.5999999999999996], [62.0, 3.7999999999999998], [75.0, 4.4000000000000004], [58.0, 3.2000000000000002], [60.0, 3.1000000000000001], [67.0, 3.7999999999999998], [68.0, 4.0999999999999996], [71.0, 4.2999999999999998], [69.0, 3.7000000000000002], [68.0, 3.5], [67.0, 3.2000000000000002], [63.0, 3.7000000000000002], [62.0, 3.2999999999999998], [60.0, 3.3999999999999999], [63.0, 4.0], [65.0, 4.0999999999999996], [67.0, 3.7999999999999998], [63.0, 3.3999999999999999], [61.0, 3.6000000000000001]] (Pdb) p array(matrix) array([[ 68. , 4.1], [ 71. , 4.6], [ 62. , 3.8], [ 75. , 4.4], [ 58. , 3.2], [ 60. , 3.1], [ 67. , 3.8], [ 68. , 4.1], [ 71. , 4.3], [ 69. , 3.7], [ 68. , 3.5], [ 67. , 3.2], [ 63. , 3.7], [ 62. , 3.3], [ 60. , 3.4], [ 63. , 4. ], [ 65. , 4.1], [ 67. , 3.8], [ 63. , 3.4], [ 61. , 3.6]]) The closest thing I could find ont the rpy list is: http://www.mail-archive.com/rpy-list@lists.sourceforge.net/msg02612.html which hints at an input conversion problem in rpy. We've got rpy 1.0.3 and R version 2.10.1 on this galaxy instance. Has anyone else seen this, or does anyone have a suggestion as to how the tool might be tweaked to bypass it? Thanks, -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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