October 2010 - galaxy-dev - lists.galaxyproject.org

conditional number of output files
by Bossers, Alex 13 Oct '10

13 Oct '10

Hi all, In my tool-config I try to use conditional number of output files. Is this possible? For input files the <CONDITIONAL> and <WHEN> statements are able to do that. What about output files? If I have four listed I will always get 4 history items in my work flow. If I only generate 3 I still get 4 items of which one contains no data. I want to prevent this cluttering by providing the user a selective set of output files. Basically can I modify the below using input parameters to generate 3 or 4 files? (not using a zip container). Any clues appreciated. <outputs> <data name="out_1" format="tabular" label="Coords" /> <data name="out_2" format="tabular" label="Delta" /> <data name="out_3" format="png" label="Plot" /> <data name="out_4" format="text" label="Console log file" /> </outputs> Alex

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quick question on building tool's interface...
by Kostas Karasavvas 13 Oct '10

13 Oct '10

Hi all, When building a tool's interface would it be possible to have a different <help></help> tag for different <param type="select"> options of a 'conditional' tag? The options change the tool parameters significantly and having a big <help> tag that includes explanation of all parameters of all the options would be a bit confusing. Thank you, Kostas

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input file properties in a tool xml file
by Marijn Vandevoorde 13 Oct '10

13 Oct '10

Dear all, Still wondering if there's a way to get the unique id that is added to a public url of a dataset. For example: mygalaxy/datasets/2e5cc78dd64522bf/display/?preview=True (I mean the 2e...). As far as I understand from the code, It's a blowfish encryption of something, not sure what exactly. In the end, I'd need to foward the actual url that allows to download the file to my tool. But of course, if I have that id, I can build the url myself. Any help's appreciated!

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tool config and fixed output file names
by Bossers, Alex 12 Oct '10

12 Oct '10

Hi all, I am probably missing something very obvious. I am struggling to make a tool config file (and/or perl/bash wrapper) that runs some tools that have several input files (no problem) but also several FIXED name output files. I am able to give it some prefix but the extensions (if any) cannot be changed. Any help appreciated how to link/get this in $output. Alex PS: sorry for cross posting users and dev. Not sure where the tool stuff belongs.

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rpy or perl
by Freddy 12 Oct '10

12 Oct '10

Hi all, Anybody some suggestions for this? Should I learn how to use rpy or simply stick with perl to get R running in galaxy. I've been browsing through the existing tool scripts in the galaxy dist, but basically everything is written in rpy to run R tools. There's 2 things I could do: either run R through perl scripts or learn rpy, which looks pretty simple at first glance. Freddy

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Managing old data
by Branden Timm 11 Oct '10

11 Oct '10

Hi All, I'm curious as to how data from old histories gets deleted. I have quite a few files built up under database/files/000, as .dat files seem to stay there even when I delete my history. What is the best practice to removing these files once they are no longer needed? Thanks -- Branden Timm btimm(a)glbrc.wisc.edu

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using csv file for importing samples
by nsfox＠uwaterloo.ca 11 Oct '10

11 Oct '10

Hi, When I try to import a sample into Galaxy using a csv file I keep getting the error "Invalid Request ID". I don't understand what a request id is (unless it's the request name) and where it is supposed to go in the sample csv file. Any suggestions as to what the "invalid request id" is referring to would be great. Thanks, Natalie

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[patch] re-fix user menu for use_remote_user = True mode
by Ry4an Brase 11 Oct '10

11 Oct '10

Back in May we submitted a tiny whitespace patch to enable some items in the user menu when use_remote_user is True, which became cset 384c809db93e. It looks like that was accidentally undone in cset 03d06d05bf62 and partially fixed in cset 5f87abcf4854 but the attached (and inlined) patch should fix the rest of it. The symptom is the absence of Histories and Datasets for users logged in when use_remote_user is True. Thanks for an awesome system, # HG changeset patch # User JJ <jj(a)msi.umn.edu> # Date 1286829453 18000 # Node ID bf6625e5007cc2b5914d04777c12d29dafa8061a # Parent 955beb170e288725ad3dc3b83e7eb6bf649e4ea5 re-fix user menu for remote user setups diff -r 955beb170e28 -r bf6625e5007c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako Fri Oct 08 16:36:16 2010 -0500 +++ b/templates/webapps/galaxy/base_panels.mako Mon Oct 11 15:37:33 2010 -0500 @@ -143,12 +143,12 @@ logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) - menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - if app.config.get_bool( 'enable_pages', False ): - menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) - if app.config.enable_api: - menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys' ), "galaxy_main" ] ) + menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) + menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) + if app.config.get_bool( 'enable_pages', False ): + menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) + if app.config.enable_api: + menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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Embed Galaxy into my own website
by Zhe Chen 11 Oct '10

11 Oct '10

Hi, Is it possible to embed Galaxy in my own website instead of embed my website into Galaxy framework? Or can I change the look and feel of Galaxy framework, such as header, footer? Thanks

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Nuitka
by Davide Cittaro 11 Oct '10

11 Oct '10

Hi all, did somebody tried this? http://kayhayen24x7.homelinux.org/blog/ d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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