Hello Wolfang,

I agree that developing the Galaxy "way" is not always "easy".  The main 
advantage of galaxy's toolshed is a point that you stated in your introduction 
"reproducibility".  Galaxy's toolshed enforces proper versioning of tool 
wrappers and its dependency on underlying software.  Hence, reproducibility is 
taken care of automatically between galaxy and the toolshed.  In addition, it  
automates one of the steps for your users: "dependencies on samtools, etc, 
etc".  Some of these dependencies are already packages in the galaxy central 
toolshed (such as samtools).  Therefore, using the tool shed is advantageous.  
Pushing the repositories to the central tool shed is a way of giving back to 
the galaxy/research community that you and I depend on.

Iyad Kandalaft

Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
KW Neatby Bldg | éd. KW Neatby 
960 Carling Ave| 960, avenue Carling
Ottawa, ON | Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel: iyad.kandal...@agr.gc.ca
Telephone | Téléphone 613- 759-1228
Facsimile | Télécopieur 613-759-1701
Government of Canada | Gouvernement du Canada

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