I've installed a local toolshed server in http://myserver/toolshed/
(served by Apache)
I am able to run it and create a repository with a tool.
In my local galaxy server (http://myserver/galaxy/) I am able to see the
repositories in that toolshed server, but when I try to install the
at InterMine we are looking to improve various aspects of our UI, and
also our interaction with Galaxy. To that end, it would be great to find
out what ways there are of depositing data in a user's account. The
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 10, 2012, at 6:47 AM, Peter Cock wrote:
I've noticed we have about a dozen stalled upload jobs on our server
from several users. e.g.
Job ID User Last Update Tool State Command Line
What does your tool shed paster log say when you get the 404 error trying to
install? You can see the paster log by running the following from your Galaxy
installation directory when your tool shed is running.
tail -f community_webapp.log
Greg Von Kuster
On Mar 16, 2012, at 4:34
The paster log from the toolshed server does not tells me much:
172.22.50.249 - - [16/Mar/2012:12:27:31 +0100] GET
HTTP/1.1 200 -
Daniel, how about your paster log from your Galaxy instance - what does it tell
you? Your logs should tell you what is causing the 404 error.
Clicking the install button when browsing the tool shed from Galaxy will
produce something like the following in your tool shed paster log:
On Feb 3, 2012, at 3:14 PM, Liisa Koski wrote:
Yes it isand my galaxy is up to date.
Sorry for not getting back to you. Did you ever figure out what was up with
this? Since you're pasting a URL, I'm wondering if the URL fetch is failing.
On Feb 7, 2012, at 5:52 AM, Federico De Masi wrote:
I have been struggling with this issue for quite a while now, and I don't
seem to find a solution (neither in situ nor in webo).
here it is:
Because of the confidentiality of our data, I have setup both a Galaxy
I have developed a Perl tool that generates a tabular file with 3
columns. I need to compare it with another tabular file (Gene Ontology
Annotation file) and I use Join, substract, group, Compare two
datasets. When I try to do so, I get the error pasted bellow. I assume
my perl code is
Database downgrade and then upgrade succeeded! galaxy instance is
On 03/15/2012 08:57 PM, Greg Von Kuster wrote:
No idea why, but for some reason your database migration script number 92
failed. You should try the following from your
I work sometimes with galaxy analysing of short reads but actually I
very much lack the function of keeping only first nucleotide of the
read in SAM file.
This is not so straightforward to do, I need to modifiy sequence,
quality scores and CIGAR.
It would be very useful for looking e.g on
Your updates that will be available for an installed repository are restricted
to the version that is installed where the version is defined by the change set
revision number. This enables different versions of tools in the repository to
always be accessible and installable.
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