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.
Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
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Government of Canada | Gouvernement du Canada
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