The Debian-Med project presents packages that are associated with
- medical informatics or
- hospital information systems
- medical imaging
- ...
- pre-clinical research, which comprises
- bioinformatics
- biochemistry
- ...
The project has a dedicated home page on http://www.debian.org/devel/debian-med/.
Over the previous years, several initiatives have spawned that address the scientific disciplines like chemistry or bioinformatics. Debian-Med is not a competition to these efforts but a platform to present the packages to the community as a CustomDebianDistribution.
Services for developers
a [http://alioth.debian.org/projects/debian-med/ Debian-Med Alioth project] which controls the access to a
subversion (svn) repository at svn://svn.debian.org/debian-med/ ([http://svn.debian.org/wsvn/debian-med web svn])
- Mailing lists
[http://lists.debian.org/debian-med/ Debian-Med] - general discussion list ([http://lists.debian.org/debian-med/ Archives])
[http://lists.alioth.debian.org/mailman/listinfo/debian-med-packaging debian-med-packaging] - reports and discussions on packages ([http://lists.alioth.debian.org/pipermail/debian-med-packaging/ Archives])
[http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit debian-med-commit] - report on commits to svn repository ([http://lists.alioth.debian.org/pipermail/debian-med-commit/ Archives])
Using subversion to edit packages
Subversion is most convenient for organizing packages as a team and even for oneself since work can continue at multiple physical locations - like work, school, public transport and home. To join in, do as follows:
set up - create aliases for the most common commands
alias svn-b='svn-buildpackage -us -uc -rfakeroot --svn-ignore' alias svn-br='svn-b --svn-dont-purge --svn-reuse' alias svn-bt='svn-buildpackage --svn-tag -rfakeroot'
The source of these aliases was lost. 'svn-b' does regularly build using the information of the repository. 'svn-br' speeds up the process by avoiding the untaring of the upstream source but is reusing the existing source tree of the prior build. The 3rd one does not need too often, don't use it, it is listed here as a reference only.
checkout everything
svn co svn://smoe-guest@svn.debian.org/debian-med/
Substitute smoe-guest with your Alioth account.- edit files and build the package with svn-b (or svn-br)
Are you a developer of Alioth and registered for DebianMed?
- No: Register yourself and ask to be added as a developer
Or: Send the result of svn diff to the Debian Med mailing list
Yes: svn commit
Whenever preparing new packages, please:
use the merge mode of subversion. From the man page: "With this method, only the debian directory (and maybe some other modified files) are stored in the repository. At build time, the contents of the svn trunk are copied to the extracted tarball contents (and can overwrite parts of it). To choose this working model, set the svn property mergeWithUpstream on the Debian directory: svn propset mergeWithUpstream 1 debian
- use patches and [dpatch]
Related pages
[http://www.debian.org/devel/debian-med/ Debian-Med home page]
?DebianMedBio
[pkg-bioc], The packaging effort for the BioConductor R libraries
- [pkg-escience], Effort to provide packages for controlling web services in bioinformatics
See also
[http://www.linuxmednews.com/ ?LinuxMedNews]