- galaxy-dev - lists.galaxyproject.org

Get job working directory
by Roberto Di Lauro 19 Jul '12

19 Jul '12

Hi all. Is there a way to get the job working directory or the job id from the implementation of "exec_before_job" hook? This hook function produces a file and I would like to store it in a job working directory. Thanks. Roberto

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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows
by Sascha Kastens 19 Jul '12

19 Jul '12

Hi! Yeah, it seems that there is now way to request the API key automatically. One simple apporach would be an extra text input field where the user has to enter his or her API key. In my use case it will be better to use a file for mapping $__user_id__ -> api_key. We run Galaxy only locally, so it would not be a security issue at all. Cheers, Sascha

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Automatic Tools installation error
by Sabbir Joy 19 Jul '12

19 Jul '12

Dear all, I am facing a uncertain problem,which i didn't face it before. Just sometimes before i have installed a new galaxy instances ,so when i logged in as an admin, i am facing a tools installation problem .i have attached the screen-shot. beside this , i turned on this line in universe.wsgi.ini tool_config_file = tool_conf.xml,shed_tool_conf.xml, still facing this problem. regards sabbirjoy

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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows
by Sascha Kastens 19 Jul '12

19 Jul '12

Hi Geert, thanks for your reply. Unfortunately it is not feasible for us to use a script outside Galaxy. As long as no official feature for Galaxy is released I will work on a script which will execute workflows via the API and add this script as a tool into Galaxy. Cheers, Sascha Original message: Hi, In case you?d be interested: we use a script that creates interlaced data of paired end data. We run this outside galaxy on groups of samples ordered in directories at once. We then import the interlaced data into galaxy, enabling batch workflow. The first step of the workflow is a deinterlacing of the datafiles. The script is available here: http://geertvandeweyer.zymichost.com/index.php?page=read&id=27 Best Regards, Geert On 07/18/2012 02:38 PM, Sascha Kastens wrote: > > Hi Dev-Team, > > are you planning or maybe working on an update which enables the > > possiblilty to run workflows in batch mode with paired end data? > > Cheers, > > Sascha > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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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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