I was trying to install release ac935c35437a. This one didn't work.
Since the release version you told me about was not the same as the one I
was trying to install, I've tried one more time to install deepTools and
finally installation has worked.
Thank you.
Best,
Stephanie
--
Stephanie Le Gras
INSERM
Computational scientist - Bioinformatician
Microarray and high throughput sequencing platform
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73
Le 29/11/13 15:08, « Bjoern Gruening » bjoern.gruen...@gmail.com a écrit
:
Hi Stephanie,
I'm facing a problem in installing a tool from the tool-shed
repository for a while now and I still don't know how to make it.
I'm trying to install deepTools
(https://github.com/fidelram/deepTools) into our Galaxy instance but I
never got the tools neither properly installed nor working.
To make a long story short :
I installed deepTools from the admin panel but got an error due to one
of the dependencies (Scipy).
Can you provide me with the exact error, please?
I solved the dependency problem, uninstalled the tool and try to
reinstall it.
When I tried to reinstall the tool, nothing happened in the panel
monitor installing tool shed repositories.
What means reinstall? You can repair a repository. You have this repair
repository action under Repository Actions.
You can also remove a repository from your installation with Deactivate
or uninstall repository under the same menue.
And when I look at what's is prompted from Galaxy logs. The same
message is prompted again and again until I leave the monitor
installing tool shed repositories page (see attached file).
That is just a webserver message, nothing from the toolshed.
I also tried to reinstall the tool from the API but I've been told
that I cannot since the tool has already been previously installed.
Is there a way to completely remove a tool from Galaxy to restart the
tool installation from the beginning?
Yes, see above. Can you tell me which exact version you have installed
from deeptools (latest version is c54d31467be4) and which version of
Galaxy you are running?
Also I released yesterday a version with pysam 0.7.7 dependency that
should fix a few pysam bugs.
Thanks for using deepTools and Galaxy,
Bjoern
Thank you in advance for your help,
Stephanie
--
Stephanie Le Gras
INSERM
Computational scientist - Bioinformatician
Microarray and high throughput sequencing platform
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73
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