Re: Possible GSoC idea: Cloud images for bioinformatics.
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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.
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