galaxy-user March 2009

galaxy-user@lists.galaxyproject.org

10 participants
16 discussions

Automating tool update
by Assaf Gordon 09 Mar '09

09 Mar '09

Hello, I have a tool which reads options from a text file (with a 'from_file' directive in the XML). A cron job regularly updates the file, and I need to reload the tool. Until recently I've used the following hack to force a tool reload (inside a shell script): ------------- wget -q -O /dev/null http://localhost:8080 --post-data="passwd=MYPASSWD&tool_id=my_tool_id&action=tool_reload" -------------- But I've recently switched to external authentication, and the above method doesn't work any more. I could try to simulate the entire user authentication process through the apache proxy, but it seems such a waste - the cron job runs on the same server as the Galaxy process. is there a better way to tell the galaxy process to reload a tool ? Thanks, Gordon.

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Re: [galaxy-user] path issue in XML tool file
by Erick Antezana 05 Mar '09

05 Mar '09

Hi Chris, Actually, I tried originally to call my programs in that way and galaxy gave me messages like this /path/to/my/tool: /path/to/my/tool: cannot execute binary file But now I tried once more and I have just realised that I forgot to delete the 'interpreter="sh"' ;-) Now it works! Thanks for the heads up! cheers, Erick > Hi Erick, > > You give paths to the scripts/binaries in the XML file e.g.: > > <command interpreter="sh">/path/to/my_script.sh -p1 $p1 -p2 $p2 -p3 > $p3</command> > > Or you can use environment variables like $PATH or $BLASTDIR. So, > there's no need for the tool to be in the same directory at all. > Cheers, > > Chris > > Erick Antezana wrote: >> Hi, >> >> while defining my own XML tool (.../galaxy/tools/my_tool.xml) I need, >> apparently?, to have a copy of the tool in the same location so that the >> XML section dedicated to call the command could find it (my_script.sh): >> >> <command interpreter="sh">my_script.sh -p1 $p1 -p2 $p2 -p3 $p3</command> >> >> is there a way to avoid such situation withou creating a wrapper and >> calling directly the tool/script? If I want to make a call to programs >> like blast, srs, etc, it won't be wise to have a copy of them in that >> location... For the moment, I created a simple shell script that >> actually >> calls the program required witht the arguments coming from galaxy... >> >> thanks, >> Erick >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)bx.psu.edu >> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > > >

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path issue in XML tool file
by Erick Antezana 05 Mar '09

05 Mar '09

Hi, while defining my own XML tool (.../galaxy/tools/my_tool.xml) I need, apparently?, to have a copy of the tool in the same location so that the XML section dedicated to call the command could find it (my_script.sh): <command interpreter="sh">my_script.sh -p1 $p1 -p2 $p2 -p3 $p3</command> is there a way to avoid such situation withou creating a wrapper and calling directly the tool/script? If I want to make a call to programs like blast, srs, etc, it won't be wise to have a copy of them in that location... For the moment, I created a simple shell script that actually calls the program required witht the arguments coming from galaxy... thanks, Erick

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Canales, Roger is out of the office.
by Roger D Canales 03 Mar '09

03 Mar '09

I will be out of the office starting 02/28/2009 and will not return until 03/16/2009. Please expect delays in response time.

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Re: [galaxy-user] galaxy update
by Greg Von Kuster 03 Mar '09

03 Mar '09

Hello Erick, OK, instead of checking out a new clone, simply update your existing clone. In your existing repo with rev 1676, perform an "hg pull -u" to update that repo with the latest code. The latest rev includes several new tools, so check the tool_conf.xml.sample file, and add new tools to your tool_conf.xml file if you want. Also, new datatypes are supported, so note any differences between datatype_conf.xml.sample and datatypes_conf.xml, adding the new supported formats to the latter. Let me know if you have any problems. Greg Von Kuster Galaxy Development Team Erick Antezana wrote: > Greg, > > the old one says: > > changeset: 1676:b83da0b74595 > tag: tip > user: guru > date: Wed Dec 17 12:13:38 2008 -0500 > summary: speed enhancement for incorrect_gops_jobs script. > > my new galaxy says: > > changeset: 1735:9fb93cfc2449 > tag: tip > user: Greg Von Kuster <greg(a)bx.psu.edu> > date: Thu Feb 19 16:25:05 2009 -0500 > summary: Fix for displaying a history's activatable datasets. > > thanks, > Erick > > >> Hello Erick, >> >> Please run "hg heads" on your repo, and reply back with the info. Thanks >> >> Erick Antezana wrote: >> >>> Hi Greg, >>> >>> >>> >>>> Hello Erick, >>>> >>>> From what repository did you get the update, and what revision did you >>>> >>>> >>> I got it yesterday from the mercurial one >>> (http://www.bx.psu.edu/hg/galaxy). I installed it in a different >>> location >>> (with different port [8081])... the contents of the Revision file is: >>> >>> Path: . >>> URL: >>> svn+ssh://coltrane.bx.psu.edu/depot/projects/universe/svnroot/galaxy/trunk >>> Repository UUID: 9bcadc22-80f8-0310-8a53-c8f022958886 >>> Revision: 1349 >>> Node Kind: directory >>> Schedule: normal >>> Last Changed Author: jbhe >>> Last Changed Rev: 1349 >>> Last Changed Date: 2007-02-08 15:12:40 -0500 (Thu, 08 Feb 2007) >>> Properties Last Updated: 2007-01-31 22:47:34 -0500 (Wed, 31 Jan 2007) >>> >>> >>> >>>> get? What was your old revision that you were updating? >>>> >>>> >>> my old revision was obtained (from mercurial too) last 18 December, this >>> is the contents of the Revision file: >>> >>> URL: >>> svn+ssh://coltrane.bx.psu.edu/depot/projects/universe/svnroot/galaxy/trunk >>> Repository UUID: 9bcadc22-80f8-0310-8a53-c8f022958886 >>> Revision: 1349 >>> Node Kind: directory >>> Schedule: normal >>> Last Changed Author: jbhe >>> Last Changed Rev: 1349 >>> Last Changed Date: 2007-02-08 15:12:40 -0500 (Thu, 08 Feb 2007) >>> Properties Last Updated: 2007-01-31 22:47:34 -0500 (Wed, 31 Jan 2007) >>> >>> both are identical...the only info I have is the dates I got them... >>> actually, the home page of both of my Galaxy installations show at the >>> very bottom the string: >>> >>> Galaxy build: $Rev$ >>> >>> but no REVISION is shown :-( maybe that should be fixed... >>> >>> thanks, >>> Erick >>> >>> >>> >>>> Greg Von Kuster >>>> Galaxy Development Team >>>> >>>> Erick Antezana wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> I have just updated my galaxy install. I was wondering if I can keep >>>>> the >>>>> database (users, workflows, etc) from my old install and use them >>>>> within >>>>> the new galaxy. Any suggestions to perform this operation so that the >>>>> new galaxy makes use of all the data/analyses previously done? is >>>>> there >>>>> any incompatibility issue? >>>>> >>>>> thanks, >>>>> Erick >>>>> >>>>> _______________________________________________ >>>>> galaxy-user mailing list >>>>> galaxy-user(a)bx.psu.edu >>>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >>> >>> > > > > >

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galaxy update
by Erick Antezana 03 Mar '09

03 Mar '09

Hi, I have just updated my galaxy install. I was wondering if I can keep the database (users, workflows, etc) from my old install and use them within the new galaxy. Any suggestions to perform this operation so that the new galaxy makes use of all the data/analyses previously done? is there any incompatibility issue? thanks, Erick

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galaxy-user March 2009