[med-svn] [Debian Wiki] Update of "DebianMed/Ensembl" by SteffenMoeller

[Debian Wiki]

Dear Wiki user,

You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification.

The "DebianMed/Ensembl" page has been changed by SteffenMoeller:
http://wiki.debian.org/DebianMed/Ensembl

Comment:
First shot at an Ensembl support page

New page:
Ensembl [1] is the name of a project and its product to store genome information on vertebrates and other eukaryotic species. It is used in many different ways by many different group with adoptions for plants or pathogens. For the production of the database, from raw sequences (traces) via assembly to the annotated genome and proteome, a series of tools from biological sequence analysis is used. Quite some have been produced by Ensembl developers themselves and made available to the public.

The Ensembl package installs the Perl-based web portal to the local computer. Except for a few local databases for handling user interactions, all data is accessed on the public database server of Ensembl. This allows the exploration and modification of server code for one's own needs, e.g. the inclusion of private data, and grants the Debian community time to steadily complete workflows for eventually reproducing the complete Ensembl pipeline. 

= Package build instructions =

 1. Checkout either full Debian Med SVN or just the tree for ensembl
  * get an account on [[http://alioth.debian.org]]
  * [[https://alioth.debian.org/account/login.php?triggered=1&return_to=%2Fproject%2Frequest.php%3Fgroup_id%3D30063|join]] the [[https://alioth.debian.org/projects/debian-med|Debian Med project]]
  * {{{svn checkout yourname-guest at svn.debian.org/svn/debian-med/trunk/packages/ensembl/ensembl/trunk ensembl}}}
 1. {{{cd ensembl}}} - the packaging root directory, containing the debian/ directory, nothing else
 1. {{{make -f debian/rules get-orig-source}}} - will create the source tarball
 1. Check and install build dependencies in debian/control.
 1. {{{svn-buildpackage -rfakeroot -uc -us}}} - builds the package
 1. {{{lintian ../build-area/*.changes}}} - generator of ideas what to work on

= Installation =

To get the package installed, add the experimental section to /etc/apt/sources.list and run {{{apt-get install -t experimental ensembl}}}. Unless you have a minimal installation of Debian, this installation is likely to conflict with a series of Perl modules. Fixing that is a major aim of our community.

= See also =

* [[http://www.ensembl.org]] Ensembl home page