Unable to add tools from tool shed
I'm following the guide on https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to add a tool from the tool shed. The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using 'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I then select to have it installed in 'NGS: Mapping' tool panel, then click Install. The page then shows two tools: bwa_mem, and package_bwa_0_7_7. Both of which show 'Error' as the status. Clicking on 'bwa_mem' shows some information with "This repository is not installed correctly (see the Repository Installation Error below)...." What does this mean? And how do I fix it?
Is there a actually a "Repository Installation Error below" - it is hard to say what went wrong without more logging? It is certainly frustrating that that package installation is failing - it seems to be a quite straight-forward installation definition. -John On Thu, Nov 13, 2014 at 3:19 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
I'm following the guide on https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to add a tool from the tool shed.
The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using 'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I then select to have it installed in 'NGS: Mapping' tool panel, then click Install.
The page then shows two tools: bwa_mem, and package_bwa_0_7_7. Both of which show 'Error' as the status. Clicking on 'bwa_mem' shows some information with "This repository is not installed correctly (see the Repository Installation Error below)...."
What does this mean? And how do I fix it?
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The tutorial uses bwa_base from the Test ToolShed which is not on Main, however I just tested bwa_mem from the Main ToolShed and it installed correctly. Please send us more information about the error you are encountering. In the Manage installed tool shed repositories <http://martenson.bx.psu.edu:8080/admin_toolshed/browse_repositories> menu item you can click on the tool in the error state and it will give you more information to send us. Thanks M. On Fri, Nov 21, 2014 at 12:15 PM, John Chilton <jmchilton@gmail.com> wrote:
Is there a actually a "Repository Installation Error below" - it is hard to say what went wrong without more logging?
It is certainly frustrating that that package installation is failing - it seems to be a quite straight-forward installation definition.
-John
On Thu, Nov 13, 2014 at 3:19 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
I'm following the guide on https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to add a tool from the tool shed.
The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using 'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I then select to have it installed in 'NGS: Mapping' tool panel, then click Install.
The page then shows two tools: bwa_mem, and package_bwa_0_7_7. Both of which show 'Error' as the status. Clicking on 'bwa_mem' shows some information with "This repository is not installed correctly (see the Repository Installation Error below)...."
What does this mean? And how do I fix it?
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Sorry for the late response to this. Under installation Status, it just says "Error". There is no actual error message shown or link available. There is a "?" next to the name. The description below the tools says "Unable to get information from the Tool shed". I checked paster.log, but don't see any error there. On Fri, Nov 21, 2014 at 12:32 PM, Martin Čech <marten@bx.psu.edu> wrote:
The tutorial uses bwa_base from the Test ToolShed which is not on Main, however I just tested bwa_mem from the Main ToolShed and it installed correctly.
Please send us more information about the error you are encountering. In the Manage installed tool shed repositories <http://martenson.bx.psu.edu:8080/admin_toolshed/browse_repositories> menu item you can click on the tool in the error state and it will give you more information to send us.
Thanks
M.
On Fri, Nov 21, 2014 at 12:15 PM, John Chilton <jmchilton@gmail.com> wrote:
Is there a actually a "Repository Installation Error below" - it is hard to say what went wrong without more logging?
It is certainly frustrating that that package installation is failing - it seems to be a quite straight-forward installation definition.
-John
On Thu, Nov 13, 2014 at 3:19 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
I'm following the guide on https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to add a tool from the tool shed.
The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using 'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I then select to have it installed in 'NGS: Mapping' tool panel, then click Install.
The page then shows two tools: bwa_mem, and package_bwa_0_7_7. Both of which show 'Error' as the status. Clicking on 'bwa_mem' shows some information with "This repository is not installed correctly (see the Repository Installation Error below)...."
What does this mean? And how do I fix it?
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
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John Chilton -
Martin Čech -
Ryan G