Protocol for changing the section of an installed tool shed repo
Hi all, Stupidly enough, I installed a tool shed repo under 'root' of the toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!). 1. From the admin menu, I choose to unactivate the repo (manage tool shed repo's) 2. From the admin menu, I reinstalled the tool shed from Main Tool Shed, and chose to put it under a section 'EMBOSS'. This to no avail: all tools still under root. 3. I manually edited the shed_tool_conf.xml and added the section tags 4. The section is now displayed, containing the EMBOSS tools. BUT the tools under the root of the toolbox are still there. Any assistance here? Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
Joachim, As you discovered, deactivating a repository does not give you the option to select a new tool panel section. However, if you select the option to remove the repository from disk, and then reinstall it, you will be presented with the tool panel section page, where you can uncheck the 'no changes' box and either select or create a tool panel section for the tools contained in the repository. --Dave B. On 5/8/13 09:44:57.000, Joachim Jacob | VIB | wrote:
Hi all,
Stupidly enough, I installed a tool shed repo under 'root' of the toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!).
1. From the admin menu, I choose to unactivate the repo (manage tool shed repo's) 2. From the admin menu, I reinstalled the tool shed from Main Tool Shed, and chose to put it under a section 'EMBOSS'. This to no avail: all tools still under root. 3. I manually edited the shed_tool_conf.xml and added the section tags 4. The section is now displayed, containing the EMBOSS tools. BUT the tools under the root of the toolbox are still there.
Any assistance here?
Cheers, Joachim
Hi Joachim, can you try to delete/rename integrated_tool_panel.xml, it is generated during start-up. Hope that helps, Björn
Hi all,
Stupidly enough, I installed a tool shed repo under 'root' of the toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!).
1. From the admin menu, I choose to unactivate the repo (manage tool shed repo's) 2. From the admin menu, I reinstalled the tool shed from Main Tool Shed, and chose to put it under a section 'EMBOSS'. This to no avail: all tools still under root. 3. I manually edited the shed_tool_conf.xml and added the section tags 4. The section is now displayed, containing the EMBOSS tools. BUT the tools under the root of the toolbox are still there.
Any assistance here?
Cheers, Joachim
Deleting the integrated tool panel config and retarting solved the issue. Thanks! Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 05/08/2013 04:02 PM, Björn Grüning wrote:
Hi Joachim,
can you try to delete/rename integrated_tool_panel.xml, it is generated during start-up.
Hope that helps, Björn
Hi all,
Stupidly enough, I installed a tool shed repo under 'root' of the toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!).
1. From the admin menu, I choose to unactivate the repo (manage tool shed repo's) 2. From the admin menu, I reinstalled the tool shed from Main Tool Shed, and chose to put it under a section 'EMBOSS'. This to no avail: all tools still under root. 3. I manually edited the shed_tool_conf.xml and added the section tags 4. The section is now displayed, containing the EMBOSS tools. BUT the tools under the root of the toolbox are still there.
Any assistance here?
Cheers, Joachim
participants (3)
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Björn Grüning -
Dave Bouvier -
Joachim Jacob | VIB |