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 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.

d) Say I create a workflow then install a new version of a tool within the workflow. I would like to be able to run that workflow using either version of the tool without creating a new workflow. Is this possible? To me it would make sense to again provide a drop down to select tool versions on the workflow ui just before execution.

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?

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.

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?

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?

Genome indexing:

1. I realise this is just a beta feature and it will be great when fully integrated. I tried to generate bowtie2 indexes for an installed build. I can see the job appear below the table in yellow and it contains the message "...added to the job queue to be indexed with bowtie2". However it seems to just sit there, even after restarting. Should I be able to see the job under 'manage jobs'?

2. Where are the generated indexes stored and is the .loc file automatically updated?

Workflow menus:

Would it be possible to categorise workflows the way we do with tools. I have a long list of workflows and it is sometimes difficult to find the one I need. I realise that workflows are user specific so this is not as easy to implement as with tools. Perhaps it would be possible to have category menus for published workflows at least?


I have noticed a few bugs with trackster in the latest release (tested on Chrome and Firefox):

1. Overview button does not work
2. If I add tracks to a group and make a composite track, then showindividual tracks again I get new menu options (filters, tool, tool parameter space visualisation). None of these seem to work and trackster often stops working after doing this.

Thanks for all the effort put in to these great new features. I hope this lengthy email is helpful!

Shaun Webb
Edinburgh University

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

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