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

problems with the lefse
by nirit ron 19 Jul '12

19 Jul '12

Hi, I am using your program from my home computer (portable computer with a small screen). I can do all the lefse analysis succesfully (everything is green) but cannot open the results- I click on the results but they do not open. when I click on the 'eye' icon I do get a file, but I don't know which program is needed for it to open (word pad and acrobat reader do not open it). Please help me. Nirit Keren.

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Where does Galaxy get its TMP directory from?
by Anthonius deBoer 18 Jul '12

18 Jul '12

Hi, I am running into some out-of-disk space errors with some of my jobs and this was because the /tmp space is running out of space. I want to use a different temporary directory but I can't get GALAXY to pick up my settings... I use this in the .ini file # Temporary files are stored in this directory. new_file_path = /mnt/ngs/analysis/tdeboer/galaxy-data/database2/tmp I set my TMPDIR environment variable to something similar, but when I check what my python script is using as its temp dir I get this: print "Temp dir: %s" % tempfile.gettempdir() Temp dir: /tmp/3642962.1.all.q It seems that the SGE engine overrides the settings in GALAXY, no? So where do I set the tmp directory to be something different then /tmp? Thanks Thon

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re-writing username for login or stripping domain from remote_user?
by Smithies, Russell 18 Jul '12

18 Jul '12

I have a situation I'm sure others have faced but I can't see how to solve it without hacking the src and I'd rather not do that just yet as it complicates upgrades. We're using Apache with NTLM and "require valid user" so it's a corporate domain and only authorized users are allowed access. If I set "use_remote_user = True" on universe_wsgi.ini then users are denied as Apache is passing the domain and username e.g. REMOTE_USER = DOMAIN\\username I can't use a rewrite rule to fix it from Apache because then it's an invalid username and the user can't log into the web, and if it's passing DOMAIN\\username to Galaxy it doesn't match up with the Galaxy username so I get a 403 error. Is there a hidden option to strip the domain from the login or am I going to have to start hacking? Thanx, Russell Smithies Infrastructure Technician 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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cannot fetch egg svgfig from http://eggs.g2.bx.psu.edu
by Di Pe 18 Jul '12

18 Jul '12

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NTLM auth not passing http_remote_user?
by Smithies, Russell 17 Jul '12

17 Jul '12

It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us. Anyone else struck this and found a solution? Our apache config looks like this: <Location "/"> AuthName "Galaxy" NTLMAuth on NTLMAuthHelper "/usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp" NTLMBasicAuthoritative on AuthType NTLM require valid-user # 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> thanx, --Russell CONTENT_LENGTH '0' HTTP_ACCEPT '*/*' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en-NZ' HTTP_AUTHORIZATION 'NTLM bla bla bla' HTTP_CONNECTION 'Keep-Alive' HTTP_COOKIE '__utmc=89232139; __utma=89232139.1132753487.1341174446.1342136886.1342560287.3; __utmz=89232139.1342560287.3.3.utmcsr=gw.agresearch.co.nz|utmccn=(referral)|utmcmd=referral|utmcct=/Pages/Default.aspx; __utmb=89232139.4.10.1342560287; galaxysession=c6ca0dd bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' HTTP_HOST 'galaxy-dev.agresearch.co.nz' HTTP_REMOTE_USER '(null)' HTTP_USER_AGENT 'Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/5.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET CLR 1.1.4322; .NET4.0C; .NET4.0E; InfoPath.3)' HTTP_X_FORWARDED_FOR '147.158.129.160' HTTP_X_FORWARDED_HOST 'galaxy-dev.agresearch.co.nz' HTTP_X_FORWARDED_SERVER 'galaxy.agresearch.co.nz' ORGINAL_HTTP_HOST 'localhost:8080' ORGINAL_REMOTE_ADDR '127.0.0.1' PATH_INFO '/' REMOTE_ADDR '147.158.129.160' REQUEST_METHOD 'GET' SERVER_NAME '127.0.0.1' SERVER_PORT '8080' SERVER_PROTOCOL 'HTTP/1.1' ======================================================================= 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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Attempting to use parallelism in BWA
by Jennifer Jackson 17 Jul '12

17 Jul '12

To give this question better visibility, I am going to move it over to the galaxy-dev(a)bx.psu.edu mailing list. Thanks! Jen Galaxy team fwd from galaxy-user On 7/17/12 11:31 AM, Scott McManus wrote: > Hi Kevin- > > That's truly odd. The error happens when the offending file is imported, > which means that > it is a syntax issue that should have been seen earlier. I'll take a > look at this soon (unless someone > else beats me to it). > > In the meantime, of course, do not use the use_tasked_jobs on this > instance of Galaxy. If others > have seen similar issues, then please speak up. > > -Scott > > ------------------------------------------------------------------------ > > Hi, > > I am using Python 2.7. I am running with an hg checked out, up to > date version of "https://bitbucket.org/galaxy/galaxy-dist/". > > I am very new to Galaxy. I have an instance setup *and > running* locally. I am able to perform routine actions such as > uploading files, processing with Picard, and aligning with BWA. I > have been able to make the jobs execute out our SGE cluster. > > In order to better utilize my cluster, I attempted to enable > parallelism of the tasks that support it (such as BWA) by > configuring the *universe_wsgi.ini* file with the parameter > > use_tasked_jobs = True > > When I do this and attempt execute a BWA alignment on a 4.1Gb fastq > file, I am given the error > > > Result 256 from mv > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0: > Traceback (most recent call last): > File "./scripts/extract_dataset_part.py", line 25, in ? > import galaxy.model.mapping #need to load this before we > unpickle, in order to setup properties assigned by the mappers > File > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py", > line 13, in ? > import galaxy.datatypes.registry > File > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py", > line 146 > finally: > ^ > SyntaxError: invalid syntax > The alignment failed. > > > If you need the complete error message, contact me and I can supply > you with it. It's too large to paste in-line and attachments aren't > allowed. > > Is there more I need to do to enable parallel jobs (splitting of > input, align, then merge)? > > Any suggestions are greatly appreciated. > > Kevin > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- Jennifer Jackson http://galaxyproject.org

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GCC2012 Registration Deadline
by Dave Clements 17 Jul '12

17 Jul '12

Hello all, This is the final email reminder that the registration deadline for the 2012 Galaxy Community Conference, is at Midnight, Central US time, on Wednesday, July 18. If you aren't registered by the end of Wednesday, you will pay *double* using late/on-site registration. The deadline for booking hotel rooms at the discounted rate has been extended until July 23, or until they fill up (and it looks like they will fill up). The 2012 conference already has more content and more participants than any previous Galaxy meeting. We would love to have you join us. See http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> for details and links. Thanks, Dave C -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Galaxy crach while visualization
by Chebbi Mohamed Amine 17 Jul '12

17 Jul '12

Hello Galaxy team ! I have e strange problem whith my Galaxy trackster visualization . While viewing bookmarked regions in my visualisation the whole Galaxy process crashed and needed to be restarted, mainly when I use Chrome browser. Above the Paster.log : xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1180427&high=1181609&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] "GET /galaxy/tracks/data?chrom=chr19&low=814128&high=815310&mode=Auto&resolution=2.954022988505747&dataset_id=7710e7c5028b7c3b&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" PostgreSQL saw the crach : 2012-07-12 12:56:40 CEST LOG: could not receive data from client: Connection reset by peer 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:00:46.907 user=user database=database host=server port=33106 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:03:45.206 user=user database=database host=server port=42867 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:06:43.257 user=user database=database host=server port=56383 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.120 user=user database=database host=server port=42663 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.596 user=user database=database host=server port=42656 Thanks Amine

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getting picard tools working in a workflow with inferred index
by Langhorst, Brad 16 Jul '12

16 Jul '12

The picard based tools nicely infer a reference sequence, and still allow the user to override. However, this inference does not work in a workflow, since that select list has no value. I'm trying to come up with a clean way for the workflow logic to read the input dataset dbkeys, but I'm not sure whether I should do this in handle_unvalidated_param_values... That's where the error comes up, but I think there is probably a better place to do the lookup and avoid the error altogether. Any pointers? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

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Cufflinks reference annotation
by Irene Bassano 16 Jul '12

16 Jul '12

Hi guys, I'm new wth NGS and have few basic questions about Galaxy for RNAseq: 1. when I run Cufflinks on my TopHat accepted hits, WHEN and WHY do i have to chose a reference annotation?Results are obviously different 2.if i chose this option, which one of the 2 references I have to upload from UCSC: RefSeq Genes or Knowngenes (both under Gene and genes prediction tracks). Hope anyone can help Thanks ib

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