Differences between revisions 23 and 57 (spanning 34 versions)
Revision 23 as of 2010-02-26 12:04:28
Size: 3371
Editor: AndreasTille
Comment: Hint to DDTP
Revision 57 as of 2020-04-01 07:44:20
Size: 6198
Editor: ?MichaelCrusoe
Comment: fix NetEpi link
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 * If you know a Free Software project that might be useful for health care in any aspect and is not yet listed in our [[http://debian-med.alioth.debian.org/tasks/|task list]] just inform us by writing an e-mail to our [[http://lists.debian.org/debian-med|mailing list]]. For instance you might compare our tasks with URLs like  * Present Debian Med on social media (Blogs, Twitter/Identi.ca, Facebook)
 * Test packages in testing / unstable with your data. This helps making sure everything will work in our future stable release.
* If you know a Free Software project that might be useful for health care in any aspect and is not yet listed in our [[https://blends.debian.org/med/tasks/index|task list]] just inform us by writing an e-mail to our [[http://lists.debian.org/debian-med|mailing list]]. For instance you might compare our tasks with URLs like
  * [[http://nebc.nerc.ac.uk/tools/bio-linux/package-list|BioLinux package list]]
  * [[http://crdd.osdd.net/osddlinux/bioresource.php|OSDD Linux]]
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  * [[http://people.freebsd.org/~fenner/portsurvey/biology.html FreeBSD ports collection of biological software]]
  * [[http://www.freshports.org/biology/ BSD FreshPorts of biological adn medical software]]
  * [[http://people.freebsd.org/~fenner/portsurvey/biology.html|FreeBSD ports collection of biological software]]
  * [[http://www.freshports.org/biology/|BSD FreshPorts of biological and medical software]]
  * [[http://gentoo-overlays.zugaina.org/dberkholz/sci-biology.html.en|Gentoo packages biological software]]
  * [[http://www.eve.ucdavis.edu/rcthomson/phylis/|PhyLis: Phylogenie oriented Ubuntu derivative]]
  * [[http://seqanswers.com/forums/showthread.php?t=43|SEQanswers: The next generation sequencing community]]
  * [[http://en.wikipedia.org/wiki/Sequence_assembly|WikiPedia page about Sequence Analysis]]
  * [[http://proteomics.ucsd.edu/|Center for Computational Mass Spectrometry]]
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 * If you have some language skills you can help to translate package descriptions for the packages we maintain in Debian. To do this go to our [[http://debian-med.alioth.debian.org/ddtp.php|translation status page]] and pick a project you would like to translate. Translation marked by a red "x" are not yet available. Click on the package you might like to translate the description and then pick your language. Alternatively you might like to visit the [[http://debian-med.alioth.debian.org/tasks/|task list]] and watch out for yellow buttons in the right column of metainformation which ask for translating the description.  * If you have some language skills you can help to translate package descriptions for the packages we maintain in Debian. For translations you might like to visit the [[https://blends.debian.org/med/tasks/index|task list]] and watch out for yellow buttons in the right column of metainformation which ask for translating the description.
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  * Biology: [[http://debian-med.alioth.debian.org/tasks/bio.html#mauve|Mauve]] ( ;o) this is a rather funny name conflict here, mauve is not only a multiple genome alignment tool, but also a java library. The real link should better be to [[http://wiki.bioinformatics.org/Mauve|here]]. I left a bit puzzled now, maybe a better package name would be bio-mauve? or genome-mauve?)
  * Epidemiology: [[http://debian-med.alioth.debian.org/tasks/epi.html#netepi-analysis|NetEpi]]
  * Imaging: [[http://debian-med.alioth.debian.org/tasks/imaging.html#bioimagesuite|BioImagesuite]]
  * Practice: [[http://debian-med.alioth.debian.org/tasks/practice.html#gnumed-server|GNUmed server]]
  * Biology: [[http://blends.debian.org/med/tasks/bio#igv|"freeing" igv]]
  * Epidemiology: [[https://blends.debian.org/med/tasks/epi#netepi-analysis|NetEpi]]
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 * Make sure you [[http://cdd.alioth.debian.org/blends//ap-bts.en.html#s-howto_itp|tagged your ITP bugs properly]].
 * Make sure that your package is listed in our [[http://debian-med.alioth.debian.org/tasks/|task list]].
 * For ITPs please follow [[http://debian-med.alioth.debian.org/docs/policy.html#itp|Debian Med policy]]
 * Make sure that your package is listed in our [[https://blends.debian.org/med/tasks/index|task list]].
 * Have a look at [[http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3|the QA page]] of Debian Med packaging team
 * If you are not yet a developer but want to become a developer yourself you might like to start reading [[http://mentors.debian.net/cgi-bin/maintainer-intro|here]].
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== Debian-med on alioth ==
 * [[http://debian-med.alioth.debian.org|debian-med.alioth.debian.org]]: It is autogenerated contend from the Blend toolkit, as well as extra informations with strong ties with the revision control system (in particular, the group policy).
== Possible tasks for Debian Med sprints ==

=== Add new lintian checks ===
 * Verify that team name matches location in Vcs-* fields
 * Verify valid characters in Vcs-* fields ('<', '>' should be invalid)
 * Verify correct sequence files?

=== Create IANA Media ("MIME") types for sequence files ===

Unregistered MIME types (now called Media Types) should be registered with IANA, to make sure the name is reserved and known to everyone. See http://www.iana.org/assignments/media-types/media-types.xhtml and http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph for an example of a successful registration related to Debian Med.

With IANA Media Types it is possible to announce file format support using .desktop files allowing desktop environment can handle such files automatically. It is probably also possible to announce it without a desktop file, as can be seen in the khmer.metadata.xml file in the khmer package.

The IANA Media Type should preferably be commonly known and originate from the community using the file format, to avoid several conflicting registration requests for the same format.

Related efforts: [[https://osf.io/a6kvu/|Bioinformatics Format Standards working group]] hosted by the Open Bioinformatics Foundation

=== Fix bugs ===
You have several options to find your bug squashing target:
 * [[http://bugs.debian.org/debian-med-packaging@lists.alioth.debian.org|BTS]]
 * [[https://udd.debian.org/dmd/?email1=debian-med-packaging%40lists.alioth.debian.org&format=html#todo|Maintainer dashboard]]
 * [[https://qa.debian.org/developer.php?login=debian-med-packaging%40lists.alioth.debian.org&comaint=yes|Debian Developer's Packages Overview]]

=== Update aging packages ===
You can use this [[https://anonscm.debian.org/cgit/blends/website.git/tree/misc/sql/aging_packages_of_blend_pubmirror|script to find aging packages]] by accessing a public UDD mirror.

=== Wanted Java packages ===
 1. https://anonscm.debian.org/cgit/pkg-java/maven-scala-plugin.git
 1. https://anonscm.debian.org/cgit/pkg-java/libnetlib-java.git
 1. https://anonscm.debian.org/cgit/pkg-java/libmtj-java.git
 1. Get rid of *.jar files in https://anonscm.debian.org/cgit/debian-med/igv.git package

== Non-Debian projects at Medical Free/Libre and Open Source Software ==
The [[http://www.medfloss.org/|MedFLOSS]] project is maintaining a nice list of free medical software which is not yet available in Debian. The most interesting feature of this list is the ranking which is created by user interaction which gives some measure how attractive a project might be for users. So just visit [[http://www.medfloss.org/node/350|this page]] and find a target for Debian packaging.

How to contribute to Debian Med?

This page is for people who wonder how they could help the Debian Med project.

Users

Developers

  • Package one of the most wanted packages from each section
  • Watch the list of bugs and fix bugs or try to provide a patch.

  • For ITPs please follow Debian Med policy

  • Make sure that your package is listed in our task list.

  • Have a look at the QA page of Debian Med packaging team

  • If you are not yet a developer but want to become a developer yourself you might like to start reading here.

Possible tasks for Debian Med sprints

Add new lintian checks

  • Verify that team name matches location in Vcs-* fields
  • Verify valid characters in Vcs-* fields ('<', '>' should be invalid)

  • Verify correct sequence files?

Create IANA Media ("MIME") types for sequence files

Unregistered MIME types (now called Media Types) should be registered with IANA, to make sure the name is reserved and known to everyone. See http://www.iana.org/assignments/media-types/media-types.xhtml and http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph for an example of a successful registration related to Debian Med.

With IANA Media Types it is possible to announce file format support using .desktop files allowing desktop environment can handle such files automatically. It is probably also possible to announce it without a desktop file, as can be seen in the khmer.metadata.xml file in the khmer package.

The IANA Media Type should preferably be commonly known and originate from the community using the file format, to avoid several conflicting registration requests for the same format.

Related efforts: Bioinformatics Format Standards working group hosted by the Open Bioinformatics Foundation

Fix bugs

You have several options to find your bug squashing target:

Update aging packages

You can use this script to find aging packages by accessing a public UDD mirror.

Wanted Java packages

  1. https://anonscm.debian.org/cgit/pkg-java/maven-scala-plugin.git

  2. https://anonscm.debian.org/cgit/pkg-java/libnetlib-java.git

  3. https://anonscm.debian.org/cgit/pkg-java/libmtj-java.git

  4. Get rid of *.jar files in https://anonscm.debian.org/cgit/debian-med/igv.git package

Non-Debian projects at Medical Free/Libre and Open Source Software

The MedFLOSS project is maintaining a nice list of free medical software which is not yet available in Debian. The most interesting feature of this list is the ranking which is created by user interaction which gives some measure how attractive a project might be for users. So just visit this page and find a target for Debian packaging.