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

Galaxy strips CSS from HTML files
by Cory Spencer 03 Mar '12

03 Mar '12

Hello all - One of the Galaxy tools I've been developing generates HTML output which I'd styled using a <style>...</style> tag in the HTML header. After updating to the latest Galaxy release earlier today, the <html>, <head>...</head>, <style> and <body> tags started to get stripped from the output, rendering previously CSS styled output rather unstylish. Delving into things, I noticed a change committed in December that sanitizes the output for HTML files via a call to "sanitize_html": https://bitbucket.org/galaxy/galaxy-central/changeset/35fee32991ce#chg-lib/… The added lines 381 -> 383 in the new file appear to be causing this new behaviour. Is there any option for making this optional? What was the rational behind stripping out these tags on outputted HTML files? Thanks for any help! Cory Spencer

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en/disable field based on the state of checkbox/radiobutton
by Keith Sheppard 01 Mar '12

01 Mar '12

Hello, From looking at the documentation for tool config syntax and I wasn't able to spot a way to have a field enabled or disabled based on the state of a radio button or checkbox. Is this possible? If I missed the documentation please point me in the right direction. I have two use cases for this: the first is that I want the user to be able to either select from a group of preselected values (in my case genome lengths) or enter their own value in a numeric field; the second is that I'd like the user to be able to select from a data file that has been stored on our server or a data file from their history. Thank you, Keith

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March 2012 Galaxy Update
by Dave Clements 01 Mar '12

01 Mar '12

Hello all, The March 2012 Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02>is now available. *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#New_Papers> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Who.27s_Hiring>at four different institutions - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Upcoming_Events_and_Deadlin…> - GCC2012 Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#GCC2012_Update>, including - Abstract submission is open. - Training Day topics are set. - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Tool_Shed_Contributions> If you have anything you would like to see in the April *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave C. -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Problem previewing a tool in the Toolshed
by Carlos Borroto 01 Mar '12

01 Mar '12

Hi, I'm currently developing my first Galaxy tool. I'm working on a wrapper for R's library cummeRbund[1]. I got to the point where the tool although incomplete on functionality, I think is ready to be uploaded to the Toolshed. I was able to do so. I also made sure I could then install it on my local instance using the toolshed repository. Everything is working as expected, except, the tool preview is not working correctly. There is no error, but the inputs, most of them conditional inputs, aren't being displayed correctly. This is the direct link to the tool in the test toolshed: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?operation=vi… [1]http://compbio.mit.edu/cummeRbund/ Kind regards, Carlos

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mrFAST web interface definition file.
by Luobin Yang 29 Feb '12

29 Feb '12

I noticed that mrFAST is listed in the Galaxy tool shed, but the downloadable files are the source code of mrFAST program itself instead of the web interface XML file. Does mrFAST have a web interface definition file and a possible wrapper program? Thanks, Luobin

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Galaxy-Development site error
by Iry Witham 29 Feb '12

29 Feb '12

Good Morning, I have been attempting to go to the the Galaxy-Dev site this morning at http://gmod.827538.n3.nabble.com/Galaxy-Development-f815885.html and Get a "Content Encoding Error" message. The error says that "The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression". This happens with Firefox 3.6.27, but not with Crome or Safari. By default I use Firefox 3.6.x due to performance issues with the later versions. Thanks, Iry Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org

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Tutorials for SICER
by Vidya .H.K 29 Feb '12

29 Feb '12

Hi, I am exploring SICER peak calling tool for ChIP seq data analysis. Can anyone suggest me tutorial site for galaxy SICER tool?? Regards H.K.VIDYA

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Timeout and Galaxy - Cluster could not complete job
by Aurélien Bernard 29 Feb '12

29 Feb '12

Hello everybody :) Today, I have a question related to timeout management in Galaxy. More particularly, I'm searching for a way to set (in a configuration file if possible) all timeouts related to DRMAA and timeouts related to communication between Galaxy and SGE. My goal is to increase current timeouts to avoid the "Cluster could not complete job" error on successful jobs when there is a temporary problem of "job status checking" (due to heavy write load on the hard drive or whatever). Is this possible ? Thank you in advance, Have a nice day A. Bernard -- Aurélien Bernard IE Bioprogrammeur - CNRS Université des sciences Montpellier II Institut des Sciences de l'Evolution France

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[API] allow_user_impersonation
by Louise-Amélie Schmitt 28 Feb '12

28 Feb '12

Hello everyone! I just wanted to know if the user impersonation will be available through the API someday :) It could be veeery useful for triggering automatic QA on the data without having to share the resulting histories afterwards. Best regards, L-A

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limited tool shed browse
by David Hoover 28 Feb '12

28 Feb '12

When I click on Admin->'Search and browse tool sheds'->'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories. However, if I search for valid tools using the menu under 'Galaxy main tool shed', I can get to any of the repositories listed at the Galaxy main toolshed. Is this a bug or a feature? David Hoover Helix Systems Staff

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