Re: [galaxy-dev] galaxy-dev Digest
Hello there, Hope this is the right mailing list. Where can I find a detailed explanation of the "track" options when selecting a particular "group" in the UCSC main Table Browser. E.g: If I choose "group: "Genes and gene prediction track", what is the difference between the various tracks listed? The UCSC website does not give a detailed explanation of the differences between the various options. And outputs change depending on this. Thanks, Irene -------------------------- Irene, What you want is a tutorial for the UCSC table browser. Something like this will help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Clicking on the button 'describe table schema' provides additional information about the tracks's content. In the future, please email the galaxy-user mailing list with questions such as these. This email list goes to the entire Galaxy team and community, so you're likely to get quicker and more complete replies there. http://wiki.g2.bx.psu.edu/Mailing%20Lists Best, J. On Jul 8, 2012, at 6:28 AM, Irene Bassano wrote: Hi Jeremy, I am new with the Galaxy system and I was wondering if there is a web site which explains the possible options listed in "group" and "track" when loading data from UCSC. Depending on the group, the track changes: is there any manual that explains the difference between all these options? Many thanks, Irene ________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of galaxy-dev-request@lists.bx.psu.edu [galaxy-dev-request@lists.bx.psu.edu] Sent: Sunday, July 08, 2012 5:00 PM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 11 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: galaxy-dev Digest, Vol 73, Issue 10 (Dorset, Daniel C) 2. How to add tag in tool xml file (sshashi) ---------------------------------------------------------------------- Message: 1 Date: Sat, 7 Jul 2012 14:10:45 -0500 From: "Dorset, Daniel C" <daniel.dorset@Vanderbilt.Edu> To: Iry Witham <Iry.Witham@jax.org> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10 Message-ID: <9B568B41976B54469CC6E3FD758EF83105DBFE7C24@ITS-DRWNEM10.ds.Vanderbilt.edu> Content-Type: text/plain; charset="us-ascii" ________________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of galaxy-dev-request@lists.bx.psu.edu [galaxy-dev-request@lists.bx.psu.edu] Sent: Saturday, July 07, 2012 11:00 AM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 10 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. pbs_python issues (Iry Witham) 2. Which css file does welcome.html use? (Dorset, Daniel C) 3. Re: Which css file does welcome.html use? (Jeremy Goecks) Hi Ira, I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, and I went through this process a couple of months ago. If I remember correctly, when you run your Python script, you're supposed to run it with "-e" not "?e" Assuming that you are pointing to the correct directory, it looks like everything else about your command is correct. Have you tried that? ---------------------------------------------------------------------- Message: 1 Date: Fri, 6 Jul 2012 16:32:14 +0000 From: Iry Witham <Iry.Witham@jax.org> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] pbs_python issues Message-ID: <CC1C8B4D.8EAD%iry.witham@jax.org> Content-Type: text/plain; charset="windows-1252" I am having an issue with pbs_python loading, but not submitting jobs to the cluster. The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory. Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below: galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started I can't seem to get past this point since I upgraded. Can someone point me in the right direction? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). 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Irene Bassano