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
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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)
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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
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________________________________________ 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
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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?
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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
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