July 2012 - galaxy-dev - lists.galaxyproject.org

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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Interested in speaking with other institutions deploying Galaxy locally?
by Ann Black-Ziegelbein 05 Jul '12

05 Jul '12

Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein

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Looking for recommendations: How to run galaxy workflows in batch
by Dave Lin 05 Jul '12

05 Jul '12

Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave

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Liftover tool installation woes
by Kwon SoonJae 05 Jul '12

05 Jul '12

Hi Everyone, I installed a local instance of galaxy and some tools using the command line, and for some reason liftover will work in the command line but won't work in galaxy. Here's what I've done so far: - Downloaded liftover standalone executable from the tool-dependencies page in the Gwiki. - Changed permissions on liftover executable to make it usable in the command prompt (terminal, macosx) -> otherwise I get permission denied. - Copied executable over to /usr/local/bin likewise to use in command prompt and in Galaxy. - Modified liftover.loc to include all the conversion types and directories of chain.gz files I downloaded to use with the tool (I believe liftover can make use of both .chain and .chain.gz files). After that I tried to run liftover in Galaxy and it didn't work, giving me some error that said hg19ToMm9 mapping is currently not available. It seems to work fine using the command line though. Since my goal is to setup galaxy locally, I really want to get this working correctly. Can anyone guide me through what's gone wrong? Also, there must be a better way of installing all these tools than manually downloading every single one and using the command line, surely? I had to type out the format of liftover.loc file manually for around 130 chain files... I'm convinced there has to be a better way. Thanks in advance, SJ

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Display with IGV local
by Chebbi Mohamed Amine 05 Jul '12

05 Jul '12

HI Galaxy-team ! I 'am trying to display BAM files whith the * local* IGV. However D*isplay with IGV "local*" use the already running copy of IGV on the server machine. So I need evry time to run manually igv by the command above: java -Xmx750m -jar igv.jar Is there any way to do this automatically I guess that I have to configure bam.xml file to call "java -Xmx750m -jar igv.jar" command , when cliking on D*isplay with IGV local*. ? Thanks for help Regards Amine

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