[Blends-commit] r3230 - in /projects/med/trunk/debian-med/tasks: bio bio-dev

Mon Mar 26 08:57:32 UTC 2012

Author: tille
Date: Mon Mar 26 08:57:32 2012
New Revision: 3230

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3230
Log:
Removed extra information from now official packages

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3230&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Mar 26 08:57:32 2012
@@ -545,6 +545,15 @@
 Depends: tm-align
 
 Depends: proftmb
+
+Depends: hhsuite
+
+Depends: ffindex
+
+Suggests: blimps-utils
+
+Depends: sift
+
 
 X-Mark: Prospective packages are starting here.
 
@@ -3779,67 +3788,6 @@
  nice features, from displaying through animation to analysing.
  It can be scripted, clustered, and runs on all common OS.
 
-Depends: hhsuite
-Homepage: http://toolkit.genzentrum.lmu.de/sections/search
-License: GPL-3.0+
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/
-WNPP: 656626
-Responsible: Laszlo Kajan <lkajan at rostlab.org>
-Pkg-Description: sensitive protein sequence searching based on HMM-HMM alignment
- HH-suite is an open-source software package for sensitive protein sequence
- searching based on the pairwise alignment of hidden Markov models (HMMs).
- It contains HHsearch and HHblits among other programs and utilities.
- .
- HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
- and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
- proteins. HHsearch is often used for protein structure prediction to detect
- homologous templates and to build highly accurate query-template pairwise
- alignments for homology modeling.
- .
- HHblits can build high-quality MSAs starting from single sequences or from
- MSAs. It transforms these into a query HMM and, using an iterative search
- strategy, adds significantly similar sequences from the previous search to
- the updated query HMM for the next search iteration. Compared to PSI-BLAST,
- HHblits is faster, up to twice as sensitive and produces more accurate
- alignments.
-
-Depends: ffindex
-License: CC-BY-SA-3.0, some files GPL-2.0+
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ffindex/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ffindex/trunk/
-WNPP: 661111
-Responsible: Laszlo Kajan <lkajan at rostlab.org>
-Pkg-Description: simple index/database for huge amounts of small files
- FFindex is a very simple index/database for huge amounts of small files. The
- files are stored concatenated in one big data file, separated by '\0'. A
- second file contains a plain text index, giving name, offset and length of
- the small files. The lookup is currently done with a binary search on an
- array made from the index file.
-
-Suggests: blimps-utils
-Homepage: http://blocks.fhcrc.org/blocks/uploads/blimps
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/blimps/trunk
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/blimps/trunk/
-WNPP: 657897
-Responsible: Laszlo Kajan <lkajan at rostlab.org>
-License: FHCRC NONCOMMERCIAL LICENSE <ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/LICENSE>
-Pkg-Description: blocks database improved searcher
- BLIMPS (BLocks IMProved Searcher) is a searching tool that scores
- a protein sequence against blocks or a block against sequences.
-
-Depends: sift
-Homepage: http://sift-dna.org/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sift/trunk
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sift/trunk/
-WNPP: 660272
-Responsible: Laszlo Kajan <lkajan at rostlab.org>
-License: FHCRC NONCOMMERCIAL LICENSE <ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/LICENSE>
-Pkg-Description: predict if an amino acid substitution in a protein has phenotypic effect
- SIFT is a sequence homology-based tool that sorts intolerant from tolerant
- amino acid substitutions and predicts whether an amino acid substitution
- in a protein will have a phenotypic effect.
-
 Depends: vegan
 WNPP: 659863
 Homepage: http://vegan.r-forge.r-project.org/

Modified: projects/med/trunk/debian-med/tasks/bio-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-dev?rev=3230&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-dev (original)
+++ projects/med/trunk/debian-med/tasks/bio-dev Mon Mar 26 08:57:32 2012
@@ -102,6 +102,8 @@
 Remark: This is a part of Bioconductor project
  A nice overview about all modules of BioDonductor is given at
  http://www.bioconductor.org/packages/release/bioc/
+
+Depends: libffindex0-dev
 
 Depends: bioclipse
 Homepage: http://www.bioclipse.net/
@@ -131,19 +133,6 @@
  Memory efficient string containers, string matching algorithms, and other
  utilities, for fast manipulation of large biological sequences or sets of
  sequences.
-
-Depends: libffindex0-dev
-License: CC-BY-SA-3.0, some files GPL-2.0+
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ffindex/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ffindex/trunk/
-WNPP: 661111
-Responsible: Laszlo Kajan <lkajan at rostlab.org>
-Pkg-Description: simple index/database for huge amounts of small files
- FFindex is a very simple index/database for huge amounts of small files. The
- files are stored concatenated in one big data file, separated by '\0'. A
- second file contains a plain text index, giving name, offset and length of
- the small files. The lookup is currently done with a binary search on an
- array made from the index file.
 
 Depends: iranges
 Vcs-Git: git://git.debian.org/git/debian-med/iranges.git


