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Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
by Dorset, Daniel C 09 Jul '12

09 Jul '12

________________________________________ From: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of galaxy-dev-request(a)lists.bx.psu.edu [galaxy-dev-request(a)lists.bx.psu.edu] Sent: Saturday, July 07, 2012 11:00 AM To: galaxy-dev(a)lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 10 Send galaxy-dev mailing list submissions to galaxy-dev(a)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(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)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(a)jax.org> To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] pbs_python issues Message-ID: <CC1C8B4D.8EAD%iry.witham(a)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.

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Galaxy Czars: Doodle pool for first Teleconference
by Ann Black-Ziegelbein 09 Jul '12

09 Jul '12

Hi everyone - We are targeting a web conference call for Galaxy Deployers/Operators for July 9th or 10th. This teleconference will be held using Elluminate Live/Blackboard Collborate web conference - so all data (including voice) will be over the internet. We have good luck at the University of Iowa with this technology for world wide remote conferences (our Ponseti International group uses it for their large distributed collaboration and others) and we can record our session and post it for playback off of the wiki. Finding a time that will suit everyone will be a challenge. If you can take a moment to respond to the doodle poll with when you can join a web conference, it will help us find the best time for the majority: http://www.doodle.com/f4f2f37smgcv3z6n By the way, if you have not found it yet, here is a link the Galaxy Czar wiki page: http://wiki.g2.bx.psu.edu/Community/GalaxyCzars Here is a draft agenda for our first call - comments are welcome : *For our first Mtg.* * Logistics: Address how we want to tackle these calls. Go over generic agenda. Frequency of calls * Presentation: Galaxy at Iowa: Discuss our issues with big data, how NGS tools take in/output data and finding the right storage server solution. * Group Goals: what do we want to accomplish with this group beyond discussions/sharing? * Open Mic & recruit new volunteers for the next call. *My shot at a generic agenda outline - to be customized each User Group Mtg ? * 20 min: Galaxy in Our Town. - presentation from a local galaxy institution on what they are doing or a problem they are troubleshooting - or have someone walk through their use cases and pain points. 20 min: Galaxy Today/Tomorrow. - presentation on a galaxy coding item. Either from penn state team, or from someone working on a new feature or customization. 20 mins: Open Mic Discussion & make point to point connections. IE - organize smaller breakouts if someone wants to host a call specific to an issue. Thanks everyone! Ann

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Re: [galaxy-dev] galaxy-dev Digest
by Irene Bassano 09 Jul '12

09 Jul '12

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(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of galaxy-dev-request(a)lists.bx.psu.edu [galaxy-dev-request(a)lists.bx.psu.edu] Sent: Sunday, July 08, 2012 5:00 PM To: galaxy-dev(a)lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 11 Send galaxy-dev mailing list submissions to galaxy-dev(a)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(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)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(a)Vanderbilt.Edu> To: Iry Witham <Iry.Witham(a)jax.org> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10 Message-ID: <9B568B41976B54469CC6E3FD758EF83105DBFE7C24(a)ITS-DRWNEM10.ds.Vanderbilt.edu> Content-Type: text/plain; charset="us-ascii" ________________________________________ From: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of galaxy-dev-request(a)lists.bx.psu.edu [galaxy-dev-request(a)lists.bx.psu.edu] Sent: Saturday, July 07, 2012 11:00 AM To: galaxy-dev(a)lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 10 Send galaxy-dev mailing list submissions to galaxy-dev(a)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(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)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(a)jax.org> To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] pbs_python issues Message-ID: <CC1C8B4D.8EAD%iry.witham(a)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.

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Adding a new tag in galaxy
by sshashi 09 Jul '12

09 Jul '12

Hi All, I installed galaxy on local machine and i want to add a new tag in tool xml file .docs for adding new tag is not available in galaxy .if any one is working on it, plz help me in finding the solution .. 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. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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pages problems - inserting one of many datasets
by Anno Nemus 08 Jul '12

08 Jul '12

Firstly, thanks for Galaxy - it's great! I have a lot of items in various histories and I think I can reproduce what looks like 2 bugs in editing user pages, using either latest chrome and firefox on ubuntu 11.10 on Main First bug - cannot choose anything to insert to a page once the second or subsequent pages of multiple history items are showing when trying to insert a dataset into a page choose: User | saved pages Create a new page and edit content choose: insert a link to a galaxy object | insert dataset link A small window opens with the start of many pages of history items - the box is too small but if you scroll down you see Insert/Cancel action buttons Select the next page (#2) The small window opens up to the full screen - but the insert/cancel buttons are no longer there and you can scroll through the list of history items but you can't seem to get back to those buttons. Even from the second page, the browser back button takes me back to the edit page screen and the #1 link takes me back to the first page without any insert/cancel options. It seems that you can't select any dataset that's not on the first page to insert? Search can be used to limit the options and select a history item so I've managed to kind of get things to work bur ir sure isn't easy. Second bug: Once you've used the search option on the list of datasets, all the other pages of history items are gone - even if you remove the search term - it doesn't resume the paging mode properly so you have to go back to the main edit screen and start again. Thanks!

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How to add tag in tool xml file
by sshashi 08 Jul '12

08 Jul '12

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. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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Which css file does welcome.html use?
by Dorset, Daniel C 06 Jul '12

06 Jul '12

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

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can not login to workflows after postgresql setup
by J.W.F.van_der_Heijden＠lumc.nl 06 Jul '12

06 Jul '12

Hi all, I have set up postgresql to work with galaxy because the standard mysqlite didn't work with my workflow. Now that postgresql seems to be working I can not login to galaxy. When I try to login it says that it can't find my username. And also when I click "forgot password" it says: "Mail is not configured for this Galaxy instance. Please contact an administrator." Any ideas? Kind Regards Jaap

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History items get REMOVED when using the API to run workflows
by Thon Deboer 05 Jul '12

05 Jul '12

Hi, I am continueing to struggle with the API.... I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api). When I run the WF on data in the LIBRARIES everything works fine. But when I choose a HISTORY as my source of data, the WF executes fine, but the history I use is emptied of all the files in there! This is very bizarre....Any ideas what is going on here? I know not a lot of people are using the API, but it is the only way I can run paired end WF on more than a couple of samples... Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer(a)me.com LinkedIn Profile

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Has anyone implemented PINDEL as a tool in their GALAXY
by Anthonius deBoer 05 Jul '12

05 Jul '12

Hi, I am about to embark of embedding PINDEL into GALAXY since it is not available in the TOOLSHED. Before I do, I thought I check if someone has already done this and could send me their XML so I don't have to start from scratch... Thanks! Thon

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