Hi all,
I've send this to both the Galaxy and Biopython developers lists,
and hope this will make sense to both groups. If you've not heard
of Galaxy, start here: http://galaxyproject.org - while the easy to
guess Biopython website is at http://biopython.org
Brad Chapman and I are both Biopython
On Thu, Sep 12, 2013 at 2:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I was wondering if the web interface for the Tool Shed could
allow us to look back at old test results?
This would be useful in connection with explicit revisions to
the tool concerned, but also when
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
...
The Biopython packages, however, are under a dedicated
biopython account on the Galaxy Tool Shed to which
currently Bjoern, Brad and I have access to:
http://toolshed.g2.bx.psu.edu/view/biopython/
Hi Greg,
When updating the version number of a tool I noticed that, as expected, both
the old version and the new version of the tool become available in the Galaxy
environment. What I did not expect is that the new version resulted in a new
entry in the menu bar (see screenshot):
Another vote for the excellent modules system from us at AgResearch
Galaxy's dependency injection works in a similar way, without requiring
all the external dependencies. We don't need unload since we compose a
unique environment for every tool execution. This is much cleaner that
loading
Hello Pieter,
The version of mercurial you are using is likely older than version 2.2.3. See:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line
Can you check this?
Greg Von Kuster
On Sep 13, 2013, at 5:54 AM, Lukasse,
Pieter,
Thank you for this report, I have reproduced this behavior in my local
Galaxy instance. I did however notice that the tool version drop-down is
still available on the tool's page, but multiple entries in the
left-hand tool panel is not intended behavior. I've created a Trello
card to
Hello Jeremy,
Thanks a lot. That was the right parameter. :-)
Best regards,
Gromobir
There is currently no simple way to circumvent this behavior. If you want to
modify the code, take a look at display_data() in data.py -- you'll want to
bump up the max_peek_size (line 351 in -central) above
When installing Galaxy Tool Shed repositories into a local Galaxy
instance, tool shed dependecies are exchanged as an encoded python
dictionary via the HTTP GET method.
If a tool shed repository contains enough dependencies, the length
of this encoded dictionary can become extremely long. In my
Just been reading a bit more about the Galaxy packaging system. Here's a
slight modification to what I was suggesting that might fit in a bit better.
Apologies for not being more familiar with the existing system before proposing
extensions.
Recall that my goal is to support using a
I've been knocking my head over this all afternoon and I was hoping to buy a
vowel, use a lifeline, whatever.
I'm trying to use the Ember JS framework (which is very nice) for some
extensions. It relies heavily on a REST model using the same method with all
of the HTTP forms including
I'd like to propose a slightly different approach.
I don't like the idea of introducing a different type of requirement
for this because it really isn't a different type of requirement. You
are still requiring a package, you just want to use a different
mechanism to provide it.
So, instead, what
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