[med-svn] [Debian Wiki] Update of "DebianMed" by CharlesPlessy
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Sat Aug 22 02:35:19 UTC 2009
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The "DebianMed" page has been changed by CharlesPlessy:
http://wiki.debian.org/DebianMed?action=diff&rev1=68&rev2=69
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 DebianPureBlends.
* '''Website''': ''http://www.debian.org/devel/debian-med/''
+ * ''To commit changes, join the [[https://alioth.debian.org/projects/webwml/|webwml]] project on Alioth''
- * ''Debian Med members who can commit changes are:''
- * AndreasTille
- * Tobias Quathamer
- * CharlesPlessy
* '''Relevant Alioth projects''':
* ''http://alioth.debian.org/projects/debian-med''
* ''http://alioth.debian.org/projects/pkg-escience''
@@ -38, +35 @@
* [[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]])
+ * The persons who know the administrative pas
- * The persons who know the administrative password of the Alioth mailing lists are AndreasTille, CharlesPlessy and NelsonOliveira.
- * Meetings
- * [[CustomDebian/Extremadura2007]]
- === Using subversion to group-maintain 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, a nice introduction due to be merged with this one (go ahead!) was found in [[Games/VCS]]:
- 1. pre set up - install packages
- {{{
- sudo apt-get install svn-buildpackage devscripts
- }}}
- 1. 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 un''tar''ing of the upstream source but is reusing the existing source tree of the prior build. The 3^rd^ one does not need too often, don't use it, it is listed here as a reference only.
- 1. checkout everything. If you have an account on Alioth then use it if you are interested in write access to the repository (you are)
- {{{
- svn co svn+ssh://smoe-guest@svn.debian.org/svn/debian-med/
- }}}
- . Substitute smoe-guest with your Alioth account. The password you may have to enter multiple times if you do not use the {{{ssh-add}}} command. For read only access do
- {{{
- svn co svn://svn.debian.org/debian-med/
- }}}
- 1. cd to source directory underneath the {{{trunk}}} directory, and download the upstream sources with
- {{{
- echo "origDir=.." >> .svn/deb-layout && uscan --force-download
- }}}
- . You do not need to change {{{.svn/deb-layout}}} the next time you upgrade the tarball with {{{uscan}}}. (''This will only work if there is a {{{watch}}} file in trunk/debian, and if the upstream tarball is in tar.gz format. Alternatively, try {{{debian/rules get-orig-source}}} from the {{{trunk}}} directory.'')
- 1. Edit files and build the package with svn-b (or svn-br)
- 1. 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}}}
- 1. When a new version got accepted in the Debian archive, and you didn't tag the last build via
- {{{
- svn-buildpackage --svn-tag
- }}}
- . you can tag this version retroactively:
- 1. create the tags directory within your package-folder, e.g. debian-med/trunk/packages/gwyddion, if it doesn't yet exist
- {{{
- svn mkdir tags}}}
- and commit or directly type the long phrase
- {{{
- svn mkdir svn+ssh://<username>@svn.debian.org/svn/debian-med/trunk/packages/<package>/tags}}}
- 1. Then tag the release
- {{{
- svn-buildpackage --svn-tag-only --svn-noautodch}}}
- which avoids the changelog getting tagged UNRELEASED.
- === Whenever preparing new packages, please: ===
- a. use patches and [[dpatch]] or [[quilt]], so there is no or little need to tamper with upstream's files directly.
- a. Upload the new package to the repository: New packages are first submitted to the Alioth svn '''after''' that package was first successfully packaged through dpkg-buildpackage
- {{{
- aliothID="smoe-guest" # adapt to what your ID is
- svnrepos=svn+ssh://${aliothID}@svn.debian.org/svn/debian-med/trunk/packages
- svn-inject -v -o package.dsc $svnrepos}}}
- a. a. Check out the source from svn. Change directory to the folder containing the debian'' directory and 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}}}" ''
- a. If svn-b'' (see above aliases) does not find the orig.tar.gz, then help with with setting the origDir. For best compatibility with the [[uscan]] auto-downloader from the [[devscripts]] package, it is suggested to specify the folder to folders above your package's debian folder. From within the trunk folder execute: {{{echo "origDir=.." >> .svn/deb-layout}}}. To retrieve the latest version of the package, if the debian/watch file is correctly set, then execute "uscan" as usual. ''
- == 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
- * DebianMedImaging
- * [[BOINC]], the Debian packages for the Berkeley Open Infrastructure for Network Computing, fosters the active involvement in biomedical research for everybody by merely contributing CPU time.
- * [[debichem]], applications for chemistry ([[http://debichem.alioth.debian.org/|Alioth]])
- * [[http://en.wikipedia.org/wiki/List_of_open_source_healthcare_software|Quite complete list of medical software in WikiPedia]]
- == See also ==
- * The work of the Debian Med packaging team in [[http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org|Debian]] and [[https://launchpad.net/~debian-med-packaging/+packages|Ubuntu]].
- * DebianMedPastMembers.
- * DebianMedProspective: study of other workflows to solve the growth crisis that we will soon or later face.
- * Supported Open Access Journals
- * Genome Biology
- * [[http://compbiol.plosjournals.org/|PLoS Computational Biology]]
- * [[http://bioinformatics.oxfordjournals.org/|Bioinformatics]] (OUP)
- * [[http://www.biomedcentral.com/bmcbioinformatics/|BMC Bioinformatics]]
- * [[http://www.scfbm.org/|Source Code for Biology and Medicine]]
- * [[http://www.bioinfo.de/isb/|In Silico Biology]] (International Fully Free online+print Journal, most in sync with Debian's principles)
- * News sites
- * [[http://www.linuxmednews.com/|LinuxMedNews]]
- * Similar Initiatives
- * [[http://www.biopuppy.org|BioPuppy]] - Debian Med packages are transformed to a Puppy-based LiveCD
- * [[http://nebc.nox.ac.uk/biolinux.html|Bio-Linux]] .deb packages
- * [[http://www.bioinf.med.uni-goettingen.de/teaching/goebixdvd/|GoeBix]] Bioinformatics LiveDVD from Göttingen (existing)
- * [[http://open-bio.org/wiki/BOSC/liveCD|BOSC Live CD]] (planned)
- * [[http://www.randomfactory.com/lfb/lfb.html|The Linux for Biotechnology cdrom project]] (RPMs)
-
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