Hi all,

So I've gotten some simple custom tools to work on our local Galaxy,
however, I am having trouble figuring out exactly how the syntax works for
the commands and lines within the <command> tag.  E.g., I've seen #if and
#for statements and also lines using functions like "str", but I can't
really find any documentation about exactly how the syntax works.  It kinda
seems like PHP syntax, but not quite?  Anyways, any help would be highly
appreciated.  Thanks!

- Nik.


On Wed, Aug 3, 2011 at 6:20 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> 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<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> tool-data/<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> effectiveT3.loc.sample<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> tools/<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> protein_analysis/<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> effectiveT3.py<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> effectiveT3.txt<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
> effectiveT3.xml<http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=92c548528a9a67cb#>
>
>
> 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"
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>
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>


-- 
Nikhil Joshi
Bioinformatics Programmer
UC Davis Genome Center
University of California, Davis
Davis, CA
http://bioinformatics.ucdavis.edu
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