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. Regards, 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.Kandalaft@agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada