Re: [galaxy-dev] Changing Tool Shed URL

2016-10-21 Thread Martin Čech
Thank you very much for sharing Youssef. Very helpful. Martin On Fri, Oct 21, 2016 at 10:20 AM Youssef GHORBAL wrote: > Hello, > > Two other tables need to be adapated (they reference tool_id) > Table “job" and table “workflow_step” > > Youssef

Re: [galaxy-dev] Changing Tool Shed URL

2016-10-21 Thread Youssef GHORBAL
Hello, Two other tables need to be adapated (they reference tool_id) Table “job" and table “workflow_step” Youssef Ghorbal Institut Pasteur - > On 21 Oct 2016, at 00:36, Youssef Ghorbal wrote: > > Hello, > > What worked

Re: [galaxy-dev] Changing Tool Shed URL

2016-10-20 Thread Youssef GHORBAL
Hello, What worked for us was this action sequence : - stop Galaxy - update config/tool_sheds_file.xml (change the URL from the old one to the new one) - “sed” shed_tool_conf.xml to change the “guid", the tool_shed and the “file” to replace the old prefix

Re: [galaxy-dev] Changing Tool Shed URL

2016-10-20 Thread Marius van den Beek
This wouldn’t be a transfer, you would uninstall the tools coming from the old toolshed and re-install them form the new toolshed. This is only possible if these tools are available from the second toolshed. To illustrate the procedure, this is what you would do if you would take all tools from

Re: [galaxy-dev] Changing Tool Shed URL

2016-10-20 Thread Olivia Doppelt-Azeroual
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

Re: [galaxy-dev] Changing Tool Shed URL

2016-10-20 Thread Marius van den Beek
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.

[galaxy-dev] Changing Tool Shed URL

2016-10-19 Thread Youssef GHORBAL
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