[Blends-commit] r3388 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Tue Jun  5 11:22:21 2012
New Revision: 3388

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3388
Log:
apollo is now available in VCS; chado is just available as Debian package as libchado-perl (and in bio-dev)

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3388&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Tue Jun  5 11:22:21 2012
@@ -326,6 +326,8 @@
 Language: Perl
 
 Depends: anfo
+
+Depends: apollo
 
 Depends: axparafit, axpcoords
 
@@ -2756,28 +2758,6 @@
  prediction. The MediGRID requires an instant easy registration by email
  for first-time users.
 
-Depends: apollo
-Homepage: http://gmod.org/wiki/Apollo
-License: Artistic License
-Pkg-Description: genome annotation viewer and editor
- Apollo is a genome annotation viewer and editor. It was developed as a
- collaboration between the Berkeley Drosophila Genome Project (part of
- the FlyBase consortium) and The Sanger Institute in Cambridge, UK.
- Apollo allows researchers to explore genomic annotations at many levels
- of detail, and to perform expert annotation curation, all in a graphical
- environment. It was used by the FlyBase biologists to construct the
- Release 3 annotations on the finished Drosophila melanogaster genome,
- and is also a primary vehicle for sharing these annotations with the
- community. The Generic Model Organism Database (GMOD) project, which
- aims to provide a complete ready-to-use toolkit for analyzing whole
- genomes, has adopted Apollo as its annotation workbench. Apollo is a
- Java application that can be downloaded and run on Windows, Mac OS X,
- or any Unix-type system (including Linux).
-Published-Title: Apollo: a sequence annotation editor
-Published-Authors: Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME
-Published-In: Genome Biology
-Published-Year: 2002
-
 Depends: e-hive
 Homepage: http://www.ensembl.org/info/docs/eHive/index.html
 License: Not specified
@@ -2787,18 +2767,6 @@
  of both data-flow graphs and block-branch diagrams which should allow it
  to codify any program, algorithm, or parallel processing job control system.
  It is not bound to any processing 'farm' system and can be adapted to any GRID.
-
-Depends: chado
-Homepage: http://gmod.org/wiki/Chado
-License: Not specified
-Pkg-Description: relational database schema for data frequently encountered in modern biology
- Chado is a relational database schema that underlies many GMOD installations.
- It is capable of representing many of the general classes of data frequently
- encountered in modern biology such as sequence, sequence comparisons,
- phenotypes, genotypes, ontologies, publications, and phylogeny. It has been
- designed to handle complex representations of biological knowledge and should
- be considered one of the most sophisticated relational schemas currently
- available in molecular biology.
 
 Depends: cmap
 Homepage: http://gmod.org/wiki/CMap