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.  

> 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.

> e) Email alerts: I could not find an option to receive email alerts about 
> tool updates when installing via the Galaxy admin ui. Perhaps this should be 
> an option during installation.

You can currently set email alerts for specified repositories in the tool shed 
itself.  I will add it to my list to enhance the install process with this 
feature.  Thanks for the request!

> 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.

> Migrating tools:
> I upgraded to the latest dist release of galaxy and when I restarted the 
> server I expected to get a message about migrating freebayes tools. I didn't 
> see this message. Will this be because I restart using --daemon? Is it 
> advisable to therefore restart without --daemon after an upgrade to see if 
> there are any tools to be migrated?

It may be best to restart without --daemon after an upgrade.  This process 
works just like the Galaxy database migration process (but you are not forced 
to perform the tool installs), so you can do whatever you currently do to 
handle database migrations after you upgrades.  Starting with --daemon should 
still display the exception in your paster log.  Do you run multiple front end 
web servers?  If so, the exception will only be thrown from one of them.

> Shaun Webb
> Edinburgh University
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
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