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
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
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
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?
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?
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
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!
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