This is the very first post to a blog about Debian Med, a community of enthusiasts and professionals in computational biology and medical informatics. They all use the Linux distribution Debian or one of those befriended distros like Ubuntu with which Debian exchanges its packages.
The title for this post is that of an abstract just submitted to the Bioinformatics Open Source Conference (BOSC 2011) . The readers of this blog will be among the first to learn about its acceptance :) The abstract stresses that Debian Med is more than the packages contributed to Debian. It is also those packages and the individuals behind them that were only created for local use. Debian Med offers subversion and git repositories to then share that local effort, granting the technically advanced users to finish the effort or to just benefit from patches, compiler flags and the specification of build/run-time dependencies directly. This sharing is especially beneficial for a series of software packages that are available as source code but are not allowed to be redistributed as binaries - VMD comes to mind, its build instructions are here.
This blog may help with some biocomputational infotainment and insights beyond what Debian Med exchanges on its mailing list already: shall the more conventional (for us) sharing of code here be augmented with a sharing of thoughts.
Just completed building Rosetta, with build instructions here in the Debian Med subversion repository. The package I consider just fine for those interested in playing what is already available through Rosetta commons. For developers it needs some extra help for the yet to be built rosetta-dev package. Provided so far are only a package rosetta comprising everything that one gets by building with "scons bin" and rosetta-dbg to collect the debug info. There is no -doc package because that being of no particular technical merits (a script is available), it takes long and generates >700MB of data. Too much to just do it by accident with a "./debian/rules binary".
ReplyDeleteLet's hope for some fraction of the Rosetta community to bite this seed-packaging and help proceeding with its development.
A walk through for building with Rosetta is now in their forum at
ReplyDeletehttp://www.rosettacommons.org/content/debian-med-sharing-rosetta-build-experience-debian-and-ubuntu
Just finished developing Rosetta, with develop guidelines here in the Debian Med subversion database. The program I consider just excellent for those enthusiastic about enjoying what is already available through Rosetta commons. For designers it needs some additional help for the yet to be designed rosetta-dev program. Offered so far are only a program rosetta including everything that one gets by developing with "scons bin" and rosetta-dbg to gather the debug details. There is no -doc program because that being of no particular technological benefits (a program is available), it requires lengthy and produces >700MB of information. Too much to just do it by chance with a "./debian/rules binary".
ReplyDeletealle zwei tage diät