Hello Marius,
Thank you for your answer.
Are you sure that ephemeris can transfer tool from toolshed1 to
toolshed2 ? We read that it was only implemented to install tools from a
toolshed on a Galaxy.
We will try the second solution and as we already tried to manipulate
the database, we stongly agree that it is not THE solution.
Cheers,
-
Fabien and Olivia and Youssef
Le 20/10/2016 à 10:29, Marius van den Beek a écrit :
Hi Youssef,
the tool shed url is also stored in the database, that's why just changing
the shed_tool_conf.xml is not working. I think you have a bunch of
options here:
1: You can make a list of tools from that toolshed and re-install them
from the new toolshed.
https://pypi.python.org/pypi/ephemeris/
<https://pypi.python.org/pypi/ephemeris/> is a nice tool to do this
efficiently.
Galaxy is (or should be) smart enough to recognize this and will
(should) not break existing workflows and tool reruns.
2: You can setup an alias in your /etc/hosts file if only the
toolshed's URL has changed, or you can setup a proxy to forward the
requests
if also the subdirectory has changed.
3. You can try to manipulate the database directly. (But I would
seriously advise you to go with possibilities 1 or 2).
Best,
Marius
On 20 October 2016 at 00:16, Youssef GHORBAL
<youssef.ghor...@pasteur.fr <mailto:youssef.ghor...@pasteur.fr>> wrote:
Hello,
I’m wondering if there is any way to change an established
Tool Shed URL.
I have a Galaxy instance and a Tool Shed instance
(http://mytoolshed.url/xxx) A lot of tools have beed installed
from that Tool Shed inside Galaxy (tools referenced inside
workflows etc)
I want to change the Tool Shed URL from
http://mytoolshed.url/xxx to http://mytoolshed2.url/yyyy.
Galaxy and Tool Shed seems to use parts of the URL as a
guid for tools.
Tool Shed does not seem to bother to be called by either
URLs (it generates guids with the new URLs scheam for new tools
though)
Galaxy does not seem to handle it, I changed the
tool_sheds_conf.xml to point to new URL, but when I update a tool
on the Tool Shed, Galaxy gets the new version but it generates
buggy tool panel (the tool is cited twice)
I also tried to mess around with the shed_tool_conf.xml
apdapting the guids and the <tool_shed> items with no luck.
Can someone point me to the right direction ? How the
matching is done between shed_tool_conf.xml entries, the
tool_version and tool_shed_repository tables.
Thank you for your help.
Youssef Ghorbal
Institut Pasteur
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Olivia Doppelt-Azeroual, PhD
Bioinformatics Engineer
CIB - C3BI - Institut Pasteur, Paris
Email: olivia.dopp...@pasteur.fr
Tel: 01 44 38 92 15
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