- galaxy-dev - lists.galaxyproject.org

2014 Galaxy Training Survey
by Dave Clements 05 Aug '13

05 Aug '13

Hello all, The Galaxy Project is asking for your help on how we should focus our training efforts for the coming year. If you are interested in Galaxy Training, please take a few minutes to let us know what you would like to see offered, and where you would like training to be held: http://bit.ly/gxy14training Thanks in advance for your time and input, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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lessc compiler error on blue_colors.ini
by Seth Sims 05 Aug '13

05 Aug '13

Dear Galaxy devs, I am attempting to create a style directory to match my school's look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error: ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FFFFFF I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process. - Seth

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Problems with running jobs on Galaxy
by Philipp Kapranov 05 Aug '13

05 Aug '13

Hello, I have submitted some simple jobs to Galaxy Main last Friday and they are still waiting to be run. Are there any issues with the cluster? Thank you, Phil Philipp Kapranov, PhD

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History & Visualization list empty
by Benjamin Schuster-Boeckler 05 Aug '13

05 Aug '13

Hi there, I've set up a local galaxy installation that so far is working very nicely. However one little issue that I'm having is that the "Saved Visualizations" and "Saved Histories" lists are empty, even though I have multiple histories and multiple visualizations. In fact, when I choose to visualize a dataset in Trackster and select "View in saved visualization", I DO see the list of existing visualizations. Pictures attached. The identical problem appears with Histories. Any idea what the problem might be? I tried in Chrome and Safari, I logged out and back in, I restarted the server, but nothing fixed the issue... Thanks in advance for the help, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom [cid:CD86F63E-0203-45D3-8802-328573CCB3B1][cid:BECC9A41-D145-4D11-A38A-485DAAB3997E]

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Galaxy jobs running on cluster can't stop.
by shenwiyn 05 Aug '13

05 Aug '13

Hi everyone, I run my galaxy jobs of Megablast on cluster ,but when I want to kill my Megablast by clicking , the job keeps on running in my background.The job_conf.xml I set as follows: <destination id="long_jobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=72:00:00,nodes=2:ppn=8,mem=16G</param> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <tools> <tool id="megablast_wrapper" destination="long_jobs"/> </tools> Could anyone give me some help please?Thank you. shenwiyn

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Server error one LefSe
by Gil Sharon 04 Aug '13

04 Aug '13

Hi All, When using the Huttenhower LEfSe on the main, online, Galaxy I got a Server Error, (Server Error,An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)) when tried to Format data for LEfSe. Was able to successfully use it yesterday, but now it seems to be down. This happened using three different browsers and on multiple retries.. Any help is appreciated.. (is there a way of getting around that step? Other steps seem to be working fine). Gil

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How to get the data-view on local instance just like the Galaxy Main ?
by Nikhil Mallela 04 Aug '13

04 Aug '13

Hi, A few days ago, I have installed the stable release of of Galaxy local instance on my Workstation & I am running it behind Apache web server proxy . In regard to the data snapshots, I've observed that, it is much more organized on the Galaxy main rather than on my local instance. For example, Take a look at these pictures: On my local instance: [image: Inline image 1] On the Galaxy main: (also, this [image: Inline image 4] is missing on my local instance) [image: Inline image 2] Also, when I click the view [image: Inline image 3] on my local instance,the headers of the data is not corresponding to its respective columns. So, how can I fine tune these ? Thanks in advance! Nikhil. -- ------------------------------------------------------------ Nikhil Vinod Mallela, M.Sc. University of Muenster, Institute of Bioinformatics, Neil-Stensen Str. 12-14, 48149, Muenster,Germany. Tel.: +49 0251 83 50006 Fax: +49 0251 83 53005Email: mallela@uni-muenster.dehttp://complex-systems.uni-muenster.de/------------------------------------------------------------

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I wrote a small script to reload tool pages
by Ben Gift 02 Aug '13

02 Aug '13

Hi, I wanted to reload xml tool wrapper pages without using the browser. Going off of this page... http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-March/009126.html I wrote a little python script that takes the tool name (the thing at the top of the xml wrapper file) as a parameter and reloads it. Setup: Run this command *curl --cookie-jar galaxy_cookie.txt --data-ascii 'email=YOUR_EMAIL_NAME%40GMAIL.COM&webapp=galaxy&password=YOUR_PASSWORD&login_button=Login' YOUR_GALAXY_WEBPAGE/user/login <http://dev1.ab.wurnet.nl:8086/user/login>* and afterwards make sure the galaxy-cookie.txt file is in the same directory as the python script. Next, if your instance isn't on localhost:8080, update the python file and change the localhosts to your instance's address. Run the python script as ./reload_tool.py --name="your tool name" For instance I run ./reload_tool.py --name="BWA for Illumina" and it reloads it. Hopefully attachments work on the mailing list. But here's a mirror if not: http://pastebin.com/jHbbizQV

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Missing Tool Shed installation errors
by Peter Cock 02 Aug '13

02 Aug '13

Hi again, Currently under "Latest revision: installation errors' my clinod tool is listed on the Test Tool Shed, yet I don't see any errors displayed here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/deb6cb2db22b Any clues? Thanks, Peter

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Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
by Peter Cock 02 Aug '13

02 Aug '13

On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Björn, > > This one has been applied in changeset 10219:a7edac403b6c, and all of > your patches are now running on the test tool shed. > > Thanks very much, > > Greg Von Kuster Hi Greg & Björn, I think supporting reStructuredText is a good idea, but should not be done automatically, consider: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 This README file is named with the extension *.txt and does not render nicely if treated as *.rst, things like "System Message: ERROR" and "System Message: WARNING" are shown to the user. I suggest that the ToolShed only render like this if the README file is using the *.rst extension, but otherwise default to plain text (e.g. no extension or *.txt files). Thanks, Peter

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