Hi Greg,
Thanks for your answer.
I've deleted the row in the tool_shed_repository table, removed the installed
tool shed repository from disk, updated my Galaxy instance to 6629:cb458aca542e
from Galaxy central and restarted Galaxy server.
I am sorry to say but I do still have the same
Hi Anne,
From your paster log it looks like the repository is installed, but for
whatever reason your shed_tool_conf.xml file cannot be updated. I've tried
many things, but am not able to reproduce this. Can you answer the following?
Have you ever been able to install a tool from the tool
Hi Greg,
Please see below my inline answers to your questions.
On 30 Jan 2012, at 15:37, Greg Von Kuster wrote:
Hi Anne,
From your paster log it looks like the repository is installed, but for
whatever reason your shed_tool_conf.xml file cannot be updated. I've tried
many things, but am
Anne,
Thanks for all of your patience and help with this. You uncovered a problem
that is very nice to have corrected. The fix is included in change set
6634:ebf72cda61e7 on our central repository. This change set will allow you to
have section tags in your tool_conf.xml file that do not
Greg,
Thanks for your patience and help with this too!
I've upgraded to ebf72cda61e7, cleaned all up (db, tool_conf.xml and
shed_tool_conf.xml, file system) and restarted galaxy. The import of
tabular2html works without the version attribute in the section of the
tool_conf.xml file. After
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 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
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