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-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@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-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@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.dor...@vanderbilt.edu> To: Iry Witham <iry.wit...@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: <9b568b41976b54469cc6e3fd758ef83105dbfe7...@its-drwnem10.ds.vanderbilt.edu> Content-Type: text/plain; charset="us-ascii" ________________________________________ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@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-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@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.wit...@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.wit...@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). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120706/a179a808/attachment-0001.html> ------------------------------ Message: 2 Date: Fri, 6 Jul 2012 16:28:08 -0500 From: "Dorset, Daniel C" <daniel.dor...@vanderbilt.edu> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Which css file does welcome.html use? Message-ID: <9b568b41976b54469cc6e3fd758ef83105dc006...@its-drwnem10.ds.vanderbilt.edu> Content-Type: text/plain; charset="us-ascii" OK, this is ostensibly a simple question. However, I can't find the CSS file that welcome.html is using. In the HTML file, there's this line: <link rel="stylesheet" href="style/base.css" type="text/css" /> However, I don't see a directory named "style" anywhere in the galaxy directory tree. When I search for "base.css," from the root Galaxy installation directory, I get the following results: ./static/june_2007_style/blue/base.css ./static/light_hatched_style/blue/base.css ./static/light_hatched_style/green/base.css ./static/old_blue_style/base.css So I assume that one of these is being used? I do think it's strange though, that the HTML points to an apparently non-existent file and yet everything on my local instance looks identical to the Penn State Public site. Thanks, Dan -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120706/af3796a9/attachment-0001.html> ------------------------------ Message: 3 Date: Fri, 6 Jul 2012 18:12:41 -0400 From: Jeremy Goecks <jeremy.goe...@emory.edu> To: "Dorset, Daniel C" <daniel.dor...@vanderbilt.edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Which css file does welcome.html use? Message-ID: <d1013340-bd6c-475f-bd9d-979746db3...@emory.edu> Content-Type: text/plain; charset="windows-1252" The CSS files used by Galaxy, including base.css, are under ./static/june_2007_style/blue . There is a route used to point to the correct location for CSS data. Best, J. On Jul 6, 2012, at 5:28 PM, Dorset, Daniel C wrote: > OK, this is ostensibly a simple question. However, I can?t find the CSS file > that welcome.html is using. In the HTML file, there?s this line: > > <link rel="stylesheet" href="style/base.css" type="text/css" /> > > However, I don?t see a directory named ?style? anywhere in the galaxy > directory tree. When I search for ?base.css,? from the root Galaxy > installation directory, I get the following results: > > ./static/june_2007_style/blue/base.css > ./static/light_hatched_style/blue/base.css > ./static/light_hatched_style/green/base.css > ./static/old_blue_style/base.css > > So I assume that one of these is being used? I do think it?s strange though, > that the HTML points to an apparently non-existent file and yet everything on > my local instance looks identical to the Penn State Public site. > > Thanks, > > Dan > ___________________________________________________________ > 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120706/2c79482e/attachment-0001.html> ------------------------------ _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev End of galaxy-dev Digest, Vol 73, Issue 10 ****************************************** ------------------------------ Message: 2 Date: Sun, 08 Jul 2012 13:22:46 +0530 From: sshashi <ssha...@cdac.in> To: Nate Coraor <n...@bx.psu.edu>, Galaxy Dev <galaxy-...@bx.psu.edu> Subject: [galaxy-dev] How to add tag in tool xml file Message-ID: <1341733966.3610.116.ca...@sasishegar.cdacb.in> Content-Type: text/plain; charset="UTF-8" Hi, How to add a new tag in tool_xml file.is there any possibility to add a tag in tool xml file ? Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. 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