-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 22/02/13 07:50, Sascha Steinbiss wrote: > [...] >> I would like to propose a bottom-up project with the goal of >> setting an infrastructure or workflow allowing one to build and >> use easily a Debian (Med) image where given bioinformatics tools >> are available at a version selected by the user (tapping in >> snapshots.debian.org or perhaps other repository within our web >> of trust if necessary). > [...] >> What do you think ?
Hi, Charles and Sascha. I think this is very important, but I think that all you need to do is 'pin' the version of critical software if you don't want to experience version creep during a bioinformatics project. I think it is still very important to keep the rest of the instance secure and up-to-date. > Sounds useful! May I point out that there is a similar effort > already going on with Cloud BioLinux [1]. Maybe Tim has something > more to say about that? In the paper it is stated that they are > aiming to improve their collaboration with the Deb Med community. > Disclaimer: I do not have first-hand experience with Cloud > BioLinux, I just handed out some Cloud Computing papers for student > seminar assignments and that was one of them... > > [1] http://www.biomedcentral.com/1471-2105/13/42 I'm involved in Bio-Linux development, and Tim encouraged me to join Debian-Med: We want to avoid needless duplication of effort and would prefer to cooperate on Ubuntu/Debian compatible bioinformatics tools. AFAIK, Ubuntu/Debian instances can be defined in terms of their package inventory for the purposes of creating compatible instances. I've used some simple scripts based on "dpkg --get-selections" output to compare the package inventory on different systems. I used this to create an AWS Bio-Linux image before the CBL (Cloud Bio-Linux) images were made. I'm sure there are better ways of synchronising package inventories, but this simple method works for me. Initially, I used "dpkg -l" output to create instances with *exactly* the same package versions installed but, more recently, I've simply used a package name inventory instead. HTH, Tony. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJRKie2AAoJELgJ/zWjRKAew/0P/jTvcjxdxv2eR5wnAmPL7bR4 8V2CO/MFjPeFNb3j11XYDf2y3cQir8IiSmNxHbTjRXCKQmA1qH6duxq4X0ZUuZgi gAYocR9LwYl3Nxp6jH/JvIEiNdPfKgELfaU1aC22nVLd4oarMxVEFbikV1at9M/8 l3841lf2R2ZK+inXZVo7Fy3fyVJGr8n4nVo2gQ1AlpmuS6CuSxkWZ+2igmE+xSvd rHCc8OjX2w5oJU8LLfYfak7fK6T+8P9iy6YwnCmDxAOlVBx04Lqg4b31rXxS69Sl /T6JytDBwu8cVNjZtta+3kjiNQ8JqslZD0jex6aSfaXJKTuc5Fcy3Al01alqlvqb Rzv+5Ibp0t33wl+f1u1Dk9eJoDeS6FUCLkoHBHR3AN/kOV40ai38ICq+BQpT5vYm Y2L/d5x7QWg6DEp7xQLh9ShhM37rgZcRqT/kTXh5UvbDL7TbpDRBNHsuuQcVG4Jh TPwqObY5fipByO6YVck6kZgcF6lonK3ljA1UwTtLPj/tTYANWuv7WfRXNpLo9Bd9 wnJPIbXjhqdJrPPdEmEmwnpuY03J+FQDqeGwRROoZ61mB5rfTbUZOppMJia3gklU 9lFIorRYybuEf6XKsEky/doPTXMU38ZbjsW7TlIkAVRU8xrZEBcnNqQmCYRBVSLw bkYgQkwxRb70DBLQJQ+3 =puL+ -----END PGP SIGNATURE----- -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
