[Debian-med-packaging] [SCM] gmap branch, master, updated. upstream/20100309-3-g4352885

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 4352885a739f3808f0eeaf07844beb7ecb9631e0
Author: Shaun Jackman <sjackman at debian.org>
Date:   Tue May 11 11:40:18 2010 -0700

    * debian/control: Expand the description.
    * debian/copyright: Set the License to `other'.
    Change the debian/* license from GPL-3 to BSD.
    * debian/gmap.1: Add ENVIRONMENT and FILES.
    * debian/gsnap.1: Ditto.
    * debian/rules: Change GMAPDB to /var/cache/gmap, was /usr/share/gmap.

diff --git a/debian/control b/debian/control
index d8ebc0e..c219707 100644
--- a/debian/control
+++ b/debian/control
@@ -13,6 +13,14 @@ Vcs-Browser: http://git.debian.org/?p=debian-med/gmap.git
 Package: gmap
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
-Description: Align mRNA and EST sequences to a genome
- GMAP: Genomic Mapping and Alignment Program
- GSNAP: Genomic Short-read Nucleotide Alignment Program
+Description: spliced and SNP-tolerant alignment for mRNA and short reads
+ This package contains the programs GMAP and GSNAP as well as
+ utilities to manage genome databases in GMAP/GSNAP format.
+ GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
+ EST, mRNA and cDNA sequences.
+ GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
+ aligning single-end and paired-end transcriptome reads.
+ Both tools can use a database of
+ * known splice sites and identify novel splice sites.
+ * known single-nucleotide polymorphisms (SNPs).
+ GSNAP can align bisulfite-treated DNA.
diff --git a/debian/copyright b/debian/copyright
index df0a1bf..ac4c19a 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Maintainer: Thomas Wu <twu at gene.com>, Colin K. Watanabe <ckw at gene.com>
 Source: http://research-pub.gene.com/gmap/
 
 Copyright: 2005 Genentech, Inc.
-License:
+License: other
  Permission is hereby granted, free of charge, to any person obtaining
  a copy of this software and associated documentation files (the
  "Package"), to use, copy, and distribute copies of the Package,
@@ -39,6 +39,5 @@ License:
 
 Files: debian/*
 Copyright: 2010 Shaun Jackman <sjackman at debian.org>
-License: GPL-3
- On Debian systems, the full text of the GNU General Public License
- version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.
+License: BSD
+ See `/usr/share/common-licenses/BSD'.
diff --git a/debian/gmap.1 b/debian/gmap.1
index 4c4d8e7..b69cfb1 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -185,6 +185,14 @@ Show version
 .TP
 \fB\-?\fR, \fB\-\-help\fR
 Show this help message
+.SH ENVIRONMENT
+.TP
+\fBGMAPDB\fR
+genome directory (eqivalent to \fB-D\fR)
+.SH FILES
+.TP
+~/.gmaprc
+configuration file
 .SH AUTHOR
 Thomas D. Wu and Colin K. Watanabe
 .SH "REPORTING BUGS"
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index b85f34f..67c7e85 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -172,6 +172,14 @@ Show version
 .TP
 \fB\-?\fR, \fB\-\-help\fR
 Show this help message
+.SH ENVIRONMENT
+.TP
+\fBGMAPDB\fR
+genome directory (eqivalent to \fB-D\fR)
+.SH FILES
+.TP
+~/.gmaprc
+configuration file
 .SH AUTHOR
 Thomas D. Wu and Colin K. Watanabe
 .SH "REPORTING BUGS"
diff --git a/debian/rules b/debian/rules
index a8c1e29..c15901b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,7 +6,7 @@ export DH_OPTIONS
 	dh  $@
 
 override_dh_auto_configure:
-	dh_auto_configure -- --with-gmapdb=/usr/share/gmap
+	dh_auto_configure -- --with-gmapdb=/var/cache/gmap
 
 override_dh_auto_install:
 	dh_auto_install --destdir=debian/tmp

-- 
Align mRNA and EST sequences to a genome