Hello Nikhil,
I am responsible for the tool shed ( both implementation as well as
documentation ), and finally got a chance to get the wiki started yesterday
(that's why it is currently lacking in information). I will be working on the
wiki as the top priority now, so it should be fairly useful within the next day
or so. In the meantime, please feel free to direct any questions to the mail
list, and I'll answer them in short order.
Getting started with the tool shed is fairly straight-forward. You can browse
existing repositories to see how others have designed their file hierarchies.
Many very good examples of repositories have been created by Peter Cock ( his
public username on the tool shed is peterjc ), so browse some of his
repositories to get an idea. Here's a good example of a repo that includes a
single tool that uses a .loc file:
Contents:
effectivet3
tool-data/
effectiveT3.loc.sample
tools/
protein_analysis/
effectiveT3.py
effectiveT3.txt
effectiveT3.xml
You can browse repos without authenticating, but in order to create a repo,
you'll need to authenticate, so create an account on the tool shed if you don't
yet have one.
Regarding your questions about the "XML format for the XML file", the
repository is simply a container for files of any type ( tool configs, data,
binaries, python scripts, exported Galaxy workflows, etc ), so the repository
itself has no requirement for XML formats, etc. Generally, XML files will
simply be the Galaxy tool config, the syntax of which is defined on our wiki at
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
Thanks very much for you interest in the tool shed,
Greg Von Kuster
On Aug 2, 2011, at 10:36 PM, Nikhil Joshi wrote:
> Hi all,
>
> I have been using Galaxy for a few years now and I am about to start creating
> my own repositories for the new Tool Shed. However, I can't seem to find any
> good documentation on how to do that exactly. Can someone point me in the
> right direction? I need to figure out the best way to organize a repository,
> the XML format for the XML file, and any other important things that I might
> need to know? Is there a good resource for all that? The wiki has a section
> entitled "Create a new repository", but there is nothing in it. Any help
> would highly appreciated. Thanks!
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Programmer
> UC Davis Genome Center
> University of California, Davis
> Davis, CA
> http://bioinformatics.ucdavis.edu
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
