[med-svn] r7080 - trunk/packages/bioperl-run/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2011-06-18 02:42:25 +0000 (Sat, 18 Jun 2011)
New Revision: 7080

Modified:
   trunk/packages/bioperl-run/trunk/debian/control
Log:
Refreshed the list of packages for which BioPerl-Run has a wrapper.


Modified: trunk/packages/bioperl-run/trunk/debian/control
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/control	2011-06-18 00:32:07 UTC (rev 7079)
+++ trunk/packages/bioperl-run/trunk/debian/control	2011-06-18 02:42:25 UTC (rev 7080)
@@ -2,14 +2,20 @@
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 8), quilt, libmodule-build-perl
-Build-Depends-Indep: perl, bioperl (>= 1.6.0), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl,
- libarray-compare-perl, libtree-dagnode-perl
-# Here is a list of all the packages and prospective packages for which wrappers are provided.
-XS-Build-Recommends: coils, emboss, eponine, footprinter, wise, genscan, hmmer,
- pise, ensembl, fingerprintscan, prscan, repeatmasker, seg, signalp, tmhmm,
- tribe, paml, molphy, phylip, clustalw, sim4, t-coffee, blast2, fasta, lagan,
- vista-align, amap-align, blat,
-# This Perl library is needed for the network tests.
+Build-Depends-Indep: perl, bioperl (>= 1.6.9),
+# Recommended in Build.PL:
+ libalgorithm-diff-perl,
+ libipc-run-perl,
+ libio-string-perl,
+ libxml-twig-perl,
+# Not yet available: libfile-sort-perl
+# Needed for the tests, but not documented Upstream
+ libarray-compare-perl, libtree-dagnode-perl,
+# Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
+ amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
+ gmap, hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
+ samtools, sim4, t-coffee, tigr-glimmer, wise,
+# Needed for the network tests:
  libwww-perl
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
@@ -22,9 +28,20 @@
 Package: bioperl-run
 Architecture: all
 Depends: ${misc:Depends}, ${perl:Depends}, bioperl (>= 1.6.0), libbio-perl-run-perl (= ${source:Version})
-Recommends: amap-align, blast2, clustalw, emboss, ensembl, hmmer, sim4, t-coffee, wise
-Suggests: coils, eponine, footprinter, genscan, pise, fingerprintscan, prscan, repeatmasker,
- seg, signalp, tmhmm, tribe, paml, molphy, phylip, fasta, lagan, vista-align, blat
+Recommends: amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
+ gmap, hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
+ samtools, sim4, t-coffee, tigr-glimmer, wise
+Suggests: 
+# Non-Free.
+ paml, molphy, phylip,
+# Not available. 
+# blat, cap3, coils, condense, dba, drawgram, drawtree, eponine, fasta, footprinter, genemark-hmm,
+# genewise, genscan, gerp, glimmer2, hyphy, lagan, lvb, match, mcs, mdust, meme, minimo,
+# neighbor, newbler, njtree, pal2nal, phastcons, phrap, primate, prints, probalign, profile,
+# promoterwise, protdist, protpars, pseudowise, quikctree, repeatmasker, sablastplus, seg,
+# semphy, seqboot, signalp, simprot, slr, soapeu, tigr-assembler, tmhmm, tribe, trnascan, vista-align,
+# Available, but needs interactive setup.
+ ensembl
 Description: BioPerl wrappers: scripts
  Contains scripts from the the BioPerl-Run package. This package will also install all
  wrappable applications packaged in Debian. The ones that are not available or not Free are