Hello Anne,
I apologize for the delay in responding to you on this. The first issue I see
is that the revision of your local Galaxy instance implies that your repo is
not being updated from the Galaxy central repository on bitbucket.
Unfortunately in order to use the tool shed, you local
Hello Greg,
Thanks a lot for your answer and sorry for having sent two emails.
Regarding the version of our local instance, I understand perfectly that the
Galaxy distribution repository is behind the Galaxy central repository but we
would like to use Galaxy on a production server and we are
Hi Anne,
A new update to the Galaxy distribution repository is planned for today, I
believe, so unless that changes you should be able to update your Galaxy
instance either today or Monday using the distribution repository. However,
this problem will continue to exist between Galaxy instances
Hi Greg,
Thanks a lot. I have the impression from what I read on the wiki that Galaxy
will be using the tool shed to provide more flexibility in choosing tools
instead of having them bundle in the current distribution. We are very much
interested by these new features because we only use a
Hi Greg,
Thanks for your answer. I've upgraded my Galaxy instance to 56bdee21dc78 from
Galaxy central repository.
I tried again to install tabular2html from the tool shed, but I get the same
problem (Server Error when installing and shed_tool_conf.xml not updated). Here
is my log in case it
Hi everyone,
I have a *.qual file and I ran Tophat on the public galaxy server but I got
the following error. I am wondering if anyone has a solution for this.
Thank you
Input: QUAL Groomer file
Database: hg19 Full
Error:
Error in tophat:
[Tue Jan 17 10:55:08 2012] Beginning TopHat run
Hi Anne,
OK, the only other thing this could be is that the metadata column in the
tool_shed_repository database table for this repository got corrupted during
the initial install when the revision of your Galaxy instance was not up to
date. So, if the repository once again got installed on
Hi,
I have tried running (on my local instance) a number of tools
(fasta_to_tabular, tandem_repeat_finder, others) on my fasta file but keep
getting the error Error executing tool: 'fasta' after file execution. In
the log file I see this
10.1.1.119 - - [27/Jan/2012:15:47:15 -0400] GET
Hi All,
We are finally up-and-running again with the latest dist release. The previoous
version was ok but already quite old.
For our local public server at wur we are now encountering the awaited disk
space issues. as had to come some daybut sooner anyway... So we have
been cleaning
January 27, 2012 Galaxy Distribution News Brief
Complete News Brief
* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_27
Highlights:
* Important metadata and Python 2.5 support corrections
* SAMtools upgraded for version 0.1.18. Mpileup added.
* Dynamic filtering, easy color options, and
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