[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-15-g8a94679

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 8a94679e5edd27fa72308d20d161a774c6e374f5
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Apr 14 12:45:45 2012 +0200

    debian/get-orig-source - removes shipped with tophat SeqAn files.

diff --git a/debian/changelog b/debian/changelog
index 35e385d..3f9357c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -11,8 +11,9 @@ tophat (2.0.0-1) UNRELEASED; urgency=low
   * debian/control  Standards-Version: 3.9.3 Depends: bowtie2
   * debian/copyright updated Format, removed seqan copyright statements
   * debian/patches removed unneeded patches
+  * debian/get-orig-source - removes shipped with tophat SeqAn files.
 
- -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Sat, 14 Apr 2012 11:56:48 +0200
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Sat, 14 Apr 2012 12:47:32 +0200
 
 tophat (1.4.1-2) unstable; urgency=low
 
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..c766701
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,22 @@
+#!/bin/sh
+# script to download and repack source package of tophat 
+# stripping off SeqAn which is distributed in Debian.
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+    grep "Newest version on remote site is .* local version is .*" | \
+    head -n 1 | \
+    sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UPSTREAMNAME=tophat
+UPSTREAMDIR="${UPSTREAMNAME}-${VERSION}"
+tar -xzf ../${UPSTREAMDIR}.tar.gz
+
+rm -rf ${UPSTREAMDIR}/src/SeqAn-1.3
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}"
+rm -rf "${UPSTREAMDIR}"
+

-- 
A spliced read mapper for RNA-Seq