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

Which version of GATK work with Galaxy?
by Fenglou Mao 30 Nov '12

30 Nov '12

When I use an old version of GATK, it failed with a report "-nt" option was not supported, I guess old GATK does not support multi-threading. If I use a new version of GATK, it failed with a report "-et NO_ET" need a key file to work since new GATK force users to report usage unless we obtain a key file, but it seems no place for galaxy to specify the key file. Any help? Thanks, Frank

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Local Instance permissions.
by Perez, Ricardo 29 Nov '12

29 Nov '12

Hi, We are implementing a local instance of Galaxy and I had a quick question, is it wrong to give Galaxy access to the UCSC databases? Thank you for your time and patience, --Ricardo Perez

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How to Tell if Apache XSendFile is Working Properly
by greg 29 Nov '12

29 Nov '12

I just set up XSendFile on my local Galaxy install by following the instructions here: [1] http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy#Sending_files_usi… However I'm wondering how to verify that uploads are in fact using XSendFile? (Galaxy still seems to create a job after the upload and the job takes a while to run.) Thanks, -Greg

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Uploading Files on Local Cluster Install
by greg 29 Nov '12

29 Nov '12

I just finished setting up a local install on our cluster but I'm having trouble uploading files. I was able to (successfully?) upload one 160MB fasta file. But any further uploads I try, they just hang. Here's the information from the log file: paste.httpserver.ThreadPool INFO 2012-11-28 12:15:18,190 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers galaxy.tools.actions.upload_common INFO 2012-11-28 12:20:36,597 tool upload1 created job id 4 galaxy.jobs.handler INFO 2012-11-28 12:20:38,386 (4) Job dispatched galaxy.jobs.runners.drmaa INFO 2012-11-28 12:20:38,930 (4) queued as 3718641 galaxy.objectstore CRITICAL 2012-11-28 12:21:03,071 /home/galaxy/job_working_directory/000/4 delete error [Errno 39] Directory not empty: '/home/galaxy/job_working_directory/000/4' paste.httpserver.ThreadPool INFO 2012-11-28 12:21:55,763 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers paste.httpserver.ThreadPool INFO 2012-11-28 12:28:26,466 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers paste.httpserver.ThreadPool INFO 2012-11-28 12:35:09,662 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers paste.httpserver.ThreadPool INFO 2012-11-28 12:46:35,565 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers The first upload that worked was around 12:20 (above), and the second failed one was at 12:40. The log file doesn't seem to even mention it? Could that error have killed the server somehow? Let me know if I can provide more info. Thanks, Greg

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file descriptors bug
by Fabien Mareuil 29 Nov '12

29 Nov '12

Hello We found a problem when we execute a job in local mode with galaxy. When a job is running and galaxy restarted, we obtain this error : message: socket.error: [Errno 98] Address already in use All the file descriptors are passed from parent to child by default with subprocess.popen. If you want to close all file descriptors excepted stdin, stdout and stderr, you have to use the option: close_fds = True. In local.py line 84-90: proc = subprocess.Popen( args = command_line, shell = True, cwd = job_wrapper.working_directory, stdout = stdout_file, stderr = stderr_file, env = os.environ, preexec_fn = os.setpgrp, close_fds = True ) I hope this will help resolving this bug Thank you in advance. Sincerely Fabien Mareuil -- Fabien Mareuil | Centre d'Informatique pour la Biologie fabien.mareuil(a)pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux 75015 Paris, France

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Stitch Gene blocks return empty result???
by 张坤山 29 Nov '12

29 Nov '12

Hi all, I trying to stitch some MAF from bed12 file using "Stitch Gene blocks". Galaxy successfully recognized my BED file and finished stitch, but no sequence in the result. My BED file is like: chr1 14662810 14707010 TCONS_00007949 0 - 14707010 14707010 0 5 229,139,106,162,77, 0,4387,4975,8271,44123, chr1 84928679 84942052 TCONS_00027714 0 + 84942052 84942052 0 4 64,173,111,398, 0,1330,12292,12975, chr1 91200237 91254779 TCONS_00030473 0 - 91254779 91254779 0 3 285,177,104, 0,52636,54438, I choose 36 mammals to stitch blocks. Galaxy gives me result like: >mm9.TCONS_00007949 >hg19.TCONS_00007949 >panTro2.TCONS_00007949 No sequence in result.What happen?? Kunshan

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Decompression Error
by Johnson, Nathan T. (MU-Student) 29 Nov '12

29 Nov '12

Received the Following Error after uploading from FTP. I'm using Main. Error is: Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line 384, in <module> __main__() File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line 134, in add_file chunk = gzipped_file.read( CHUNK_SIZE ) File "/usr/lib/python2.7/gzip.py", line 256, in read self._read(readsize) File "/usr/lib/python2.7/gzip.py", line 307, in _read uncompress = self.decompress.decompress(buf) zlib.error: Error -3 while decompressing: invalid stored block lengths Thank you for your assistance. Nathan T. Johnson Department of Veterinary Pathobiology University of Missouri 4011 Discovery Drive Columbia, MO 65201 Lab: N152 RADIL Lab: (573)884-3429 Email: ntjxv7(a)mail.missouri.edu

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Galaxy API call workflow_execute_parameters.py
by Alex Rodriguez 29 Nov '12

29 Nov '12

Dear Galaxy developers and community, I have been testing and using the latest additions to the galaxy api calls which are great and very useful. The script workflow_execute_parameters.py is great because you can modify parameters on the fly when submitting workflows. However, I ran into a problem with this script. This script works nicely if you have to modify only one parameter per tool, however, if I have 2 or more parameters for the same tool that I need to adjust, it will only adjust one parameter, while ignoring the rest of the parameters in my list for that tool. I believe the issue has to do with line 44 in the script which reassigns the parameter name and value for a tool instead of adding to a list. Would a fix for this just be as simple as assigning a list to the dictionary of multiple parameters for the same tool? Thanks, Alex for v in sys.argv[5:]: print("Multiple arguments "); print(v); try: step, src, ds_id = v.split('='); data['ds_map'][step] = {'src':src, 'id':ds_id}; except ValueError: print("VALUE ERROR:"); wtype, wtool, wparam, wvalue = v.split('='); try: Line 44: data['parameters'][wtool] = {'param':wparam, 'value':wvalue} except ValueError: print("TOOL ID ERROR:");

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dynamic column names and R ExpressionSet files
by S. Horsman 28 Nov '12

28 Nov '12

Hi All, I'm trying to dynamically load labels from a BioConductor ExpressionSet file (binary .RData) into a select item type. This works just fine, but with a few caveats. Example (for reference, this is from a modification of https://trac.nbic.nl/galaxytools/browser/trunk/tools/proteomics/NPC/AMC/DE.…) <code file="CL_code.py"/> ... <page> <param name="eset" type="data" label="Expression set" format="rdata" force_select="True" help="An R data file containing an ExpressionSet"/> </page> <page> <param name="label" type="select" dynamic_options="get_label(eset,False,'class')" force_select="True" label="Variable to test" size="20" help="Name of the variable subject to testing" /> ... I would like to remove the deprecated page tags here (also then the tool can be added to a workflow). However if I do that and then select an ExpressionSet file, the select list does not update. It only works when loading the page for the first time, or when I use the page tags. For text files the solution would be easy; just use type="data_column" and data_ref="yourinputfileparamname" and it auto-updates the select field (though not with the actual column names but that is another issue). With a binary file this is not possible, therefore the dynamic_options feature is needed to do this. Does anyone know of a way to get this to work without using the page tags? Kind regards, Bas Horsman Dept. Bioinformatics Erasmus MC

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Problem with Active Directory/LDAP authentication
by Harris Shapiro 28 Nov '12

28 Nov '12

Hello, I'm writing because I've been trying for the past few days to configure Galaxy to use Apache-based LDAP authentication, but have reached a point where I'm basically stuck. The system in a virtual machine running: - CentOS 5.8 - Apache 2.2.3 I'm trying to configure a Galaxy instance at "localhost:8080", with Active Directory authentication. I started with the admin page documentation: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy and also worked through the troubleshooting examples found at: a) http://user.list.galaxyproject.org/Galaxy-Apache-External-Authentication-tt… b) http://gmod.827538.n3.nabble.com/galaxy-dev-ldap-integration-td839409.html c) http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-January/001676.html Following the debugging steps suggested by URL (a), I'm able to verify that: 1) The authentication clause I have works, without rewrite rules and without a proxy. 2) Without rewrite rules and a proxy, the Apache environment has the AUTHENTICATE_SAMACCOUNTNAME and REMOTE_USER environment variables set. Unfortunately, when I turn on the proxy (setting "use_remote_user" and "remote_user_maildomain" in universe_wsgi.ini accordingly), I get the following error message when I try accessing the "localhost:8080" URL, the following error message appears: "Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. Please contact your local Galaxy administrator." As suggested by URLs (a) and (c), I modified ./lib/galaxy/web/framework/middleware/remoteuser.py to print the environment seen by that script. None of the remote user information seems to be making to the script, either from AUTHENTICATE_SAMACCOUNTNAME or REMOTE_USER, no matter which of the suggested combinations of "RewriteCond", "RewriteRule", and "RequestHeader" options I tried. In addition, the troubleshooting suggestions to force a REMOTE_USER value to be set via a directive like: RequestHeader add REMOTE_USER [user name] also failed to pass REMOTE_USER to the remoteuser.py script. I've included below an extract from the Apache configuration file that I've been trying. Any advice or assistance that people might be able to provide would be greatly appreciated, and please let me know if you'd need any additional information from me. Sincerely, Harris Shapiro Genomic Health, Inc. Extract from Apache configuration file: Note: I've also tried a variant where I replaced REMOTE_USER with AUTHENTICATE_SAMACCOUNTNAME in the various RewriteCond & RequestHeader directives. That variant produced the same error message. <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> RewriteEngine on <Location "/"> AuthType Basic AuthName "Please log in with your Windows account" AuthBasicProvider ldap AuthLDAPURL [Verified LDAP connection information] AuthzLDAPAuthoritative off AuthLDAPBindDN [Verified DN] AuthLDAPBindPassword [Verified password] Require valid-user RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e </Location> RewriteRule ^/static/style/(.*) /home/hshapiro/software/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /home/hshapiro/software/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /home/hshapiro/software/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /home/hshapiro/software/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/hshapiro/software/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P]

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