Greg and Björn, thanks for the info.

I will again review that section. Indeed a simple tool just required an xml, 
tool script and some README. But as you guessed I was more interested in 
complexer types; One might be the use of a bowtie2 multi mapper script we use 
to map fastq reads to a set of databases picked from the available bowtie 
indices within galaxy. Graphs are generated with R.

So of course the xml and wrapper scripts should be there as well as the R 
How about bowtie2_db.lock additions?
How to secure R and bowtie2? Just by requirements?
And their licenses?


Van: Greg Von Kuster []
Verzonden: maandag 4 februari 2013 16:25
Aan: Bossers, Alex
Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission

Hello Alex,

In very general terms, a repository should include everything necessary for 
ensuring each if it's contained utilities is functionally correct when 
installed into a local Galaxy instance.  Categories of Galaxy utilities are 
Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 
3rd-party tool dependency definitions and repository dependency definitions.

I believe the content of the original tool shed wiki is mostly retained in the 
current wiki.  The original wiki was just divided into document sections, and a 
lot of new content has been added because of the many new tool shed features 
that have been introduced.  The main section detailing repository content it is 
  This page include many related pages whose links are at the bottom of the 

It is not possible to give a precise, but general definition of what should be 
included in all repositories because repositories can contain different types 
of Galaxy utilities.  Each of the sections of the wiki page link above 
describes how to include these various Galaxy utilities.

Even Galaxy tools fall into various categories.  For example, some are very 
simple, requiring no 3rd party tool dependencies and the tool form does not use 
dynamically generated select lists.  These generally only require a script and 
an XML file.  However, more complex Galaxy tools may require additional 
supporting content to be included in the repository (e.g., a 
tool_data_table_conf.xml.sample file. etc)

If you could provide more details about what types of utilities you are 
building, I can steer you to the wiki pages that provide information about 
those specific utilities.


Greg Von Kuster

On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:

Hi All,

We are experimenting with local toolsheds for tool maintainability. On the old 
galaxy wiki I can remember there was a short tutorial or small description of 
the minimal requirements of a tool to be submitted to the toolshed. Actually we 
submitted some.
However we seem unable to retrieve the proper info from the updated wiki.
We did find info on single tools or suites, or more special cases, but a simple 
example/list of  how and what to include in a repository is missing (at least 
we cannot find it....might be an issue of wrong key words)..

Anyone has an idea where to find such a document?


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