Hi Greg, thanks for the response

Quoting Greg Von Kuster <g...@bx.psu.edu> on Tue, 31 Jul 2012 11:50:36 -0400:

Hi Shaun,

On Jul 31, 2012, at 9:37 AM, SHAUN WEBB wrote:

Hi, I have been trying out the latest version of Galaxy and a newly installed local toolshed and I have a few questions/suggestions/bug reports:

1. Tool Versioning:

a) As I understand from the wiki, when I create a new version of a tool in a tool shed I must then install the latest version in my Galaxy instance.

This is not correct - you can choose to install any valid version of the tool(s). Can you let me know what content of the wiki resulted in this confusion? I'll be sure to make it more clear.

This then shows up as two separate tools in my tool menu. Presumably it is best to change the xml description tag to reflect the version number and make tool versions distinguishable in the Galaxy tool menu?

b) Would it make more sense to have a single entry for each tool in the tool menu and a drop down to choose which version to run in the tool gui? Similar to when I try to rerun a tool that is no longer installed I get a drop down option to use a derivative of that tool if it exists.

Your above recommendation in (b) is exactly what will occur as soon as I get a chance to implement it.

Perhaps my wording was unclear here. What I meant was if a new version of a tool is created in a tool shed I have to install that version to be able to use it, rather than using 'get updates'. This then results in multiple listings of the tool. But it sounds like you plan on improving this process anyway.

c) The toolshed interface allows me to change the name of my tool. If I do this, then go to my Galaxy admin ui and try to get updates for my tool then it fails. Does it make sense to change a tools name after it is created? Is it possible to track previous tool names to avoid this happening?

This should not occur. Where are you able to change the name of your tool? You are not even allowed to change the name of the repository if it has been cloned (you can change the name of the repository as long as it has not been cloned). Can you send me a screen shot of hte page that allows you to change the name of your tool in the tool shed? I'll provide a fix as soon as I see where the issue lies.

OK, I guess I changed the name of my repository not tool. I then installed the tool via my local Galaxy instance. I can still change the name of the repository in my toolshed and when I try to get updates via Galaxy admin panel I get the following server error: "AttributeError: 'NoneType' object has no attribute 'repo_path'"

Running toolshed tools:

I have no problems installing tools from toolsheds via Galaxy admin interface, however I can't get these tools to run. They stay Grey forever and look like this in the manage jobs table:

65 x...@xxxx.xx.ac.uk 0 minutes ago toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_counts/0.1.0 new None None None

Do I have to set a tool runner or some other option for shed_tools?

No special configuration settings are required in your local Galaxy instance to to run tools installed from a tool shed. If they stay in the queued state, there must be an issue in your local Galaxy instance that causes installed tools as well as tools included in the distribution to remain queued. It has nothing to do with the fact they were installed.

No. All other tools run fine. Tools installed from either my toolshed or the Galaxy toolshed remain queued. If this is not a known issue then I will try to dig a little deeper to find the problem. Any pointers would be useful if you can think of why there should be a difference.

Thanks for your help!

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