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
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
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
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
65 xxxx(a)xxxx.xx.ac.uk 0 minutes
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
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.
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