Hi Greg,
Thanks for this!
On 17 October 2012 01:17, Greg Von Kuster g...@bx.psu.edu wrote:
I managed to break a toolshed-installed tool by fiddling with the
files under shed_tools.
As you've discovered, this is not a good thing to try. Always use the Galaxy
interface features to perform
Hi,
I noticed that in the new Galaxy version the preview of HTML files seems to be
broken. When I try to preview a HTML file generated by a tool, it displays a
HTML that has all style stripped off. So the HTML display is in fact changing
the generated HTML before displaying it.
Has anyone
Hi,
Make sure that in your universe.wsgi is set:
sanitize_all_html = False
Hope this helps,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 10/17/2012 10:09 AM, Lukasse,
Hi,
I have a similar problem with renaming fastq to fastqsanger. In my case after
some time galaxy displays
An error occurred setting the metadata for this dataset. You may be able to set it manually or
retry auto-detection.
The paster.log shows this:
galaxy.jobs DEBUG 2012-10-17
In the main toolshed I find bam_to_bigwig 2 times.
Description, Version and Requirements seem the same.
How am I to decide which one to use?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
For info: turns out this was already reported and fixed back on the 5th
October in galaxy-central changeset 210c39f4bf7f, specifically applying
these patches:
https://bitbucket.org/galaxy/galaxy-central/changeset/029818b7e546a3b6835c49ef4f8694c5ac695dfb
fixed the problem for me. (Thanks Scott
On Wed, Oct 17, 2012 at 1:30 PM, Andreas Kuntzagk
andreas.kuntz...@mdc-berlin.de wrote:
In the main toolshed I find bam_to_bigwig 2 times.
Description, Version and Requirements seem the same.
How am I to decide which one to use?
regards, Andreas
A little history:
Brad's was first, using
Hi,
In the command tag of the tools/update.xml file, the paramfile was
setted by the result of some statements followed, I want to know what
syntax is and if it is OK that I move the statements to configfile tag?
Thanks,
welkin
___
Like most days, JJ very politely pointed out that I am a wrong this
morning. You can have variable numbers of outputs at runtime, see the
last section (Number of Output datasets cannot be determined until
tool run
) of this page:
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files
Todd, this is definitely unusual. Can you post (or send directly)
relevant sections from the Galaxy log?
-- jt
On Tue, Oct 16, 2012 at 8:15 PM, Todd Oakley
todd.oak...@lifesci.ucsb.edu wrote:
Hello,
We just did a few tweaks to improve Galaxy performance, and a new issue
popped up that I
I had an odd error with wigToBigWig that I tracked back to the *.len files
generated by the updateucsc.sh script. With my last UCSC update, a majority of
the assemblies have this as the single line:
META http-equiv=Content-Script-Type content=text/javascript
but others, like
Hi,
I was trying to upload a 43Gb BAM file to Galaxy when I encountered
this problem.
I am new to galaxy and python.
I have tried uploading files in other formats and they have worked fine.
I am using galaxy as a local installation and appreciate any thoughts
on how to fix this.
Thanks
Sukha
Hello Clare,
On Oct 17, 2012, at 2:22 AM, Clare Sloggett wrote:
Actually, the reason I did this was because I didn't know how to solve
a different problem, so maybe I should ask you about that one as well.
We had some occasions where we'd try to install a tool from the
toolshed, and it
Hello,
1. When we access galaxy (local installation) using IE (internet
explorer) 8 and 9, we cannot expand/collapse uploaded data files
visible from history window. Neither are the info and save icons
visible. How do I fix this ? Also items under the main menu are not
clickable (e.g. when I
Hello Bjorn,
From your comments, it seems you are looking for a way to define a tool
dependency that is included in the contents of the repository when it is
installed from the tool shed. If this is the case, then your
tool_dependencies.xml tag set needs to be changed to the following.
On Mon, Oct 15, 2012 at 11:49 AM, Liisa Koski liisa.ko...@basf.com wrote:
Hello,
I've installed a tool to my local Galaxy installation via my local ToolShed.
I would like to run this tool locally, and not have it submitted to the
grid.
I have tried two ids in the universe_wsgi.ini
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