Hi Alex,

On Feb 4, 2013, at 10:35 AM, Bossers, Alex wrote:

> 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 
> scripts.


R scripts are defined as tool dependencies that are contained within the same 
repository.
See 
http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time


> How about bowtie2_db.lock additions?


This is defined as a 3rd-party tool dependency, and you can include a file 
named tool_dependencies.xml that defines how to install and compile it and 
ensure your appropriate repository tool can locate the compiled dependency.
See 
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories


> How to secure R and bowtie2? Just by requirements?

Can you clarify this question?


> And their licenses?

See http://wiki.galaxyproject.org/ToolShedReadmeFiles

>  
> Thanks
> Alex
>  
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Verzonden: maandag 4 februari 2013 16:25
> Aan: Bossers, Alex
> CC: galaxy-dev@lists.bx.psu.edu
> 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 here:  
> http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
>   This page include many related pages whose links are at the bottom of the 
> page.
>  
> 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.  
>  
> Thanks!
>  
> 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?
>  
> Thanks
> Alex
>  
>  
>  
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