[med-svn] [SCM] tophat branch, master, updated. upstream/1.3.3-14-g7059312

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 82b04c498ce2c354cbfafae92c91c1a147c5a930
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 15 22:04:09 2011 +0100

    Use seqan lib from debian and not from source

diff --git a/debian/patches/debian_seqan.patch b/debian/patches/debian_seqan.patch
new file mode 100644
index 0000000..e677688
--- /dev/null
+++ b/debian/patches/debian_seqan.patch
@@ -0,0 +1,11 @@
+--- tophat.orig/configure.ac
++++ tophat/configure.ac
+@@ -117,7 +117,7 @@
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
+ CXXFLAGS="$CFLAGS $BAM_CPPFLAGS"
+ 
+-AM_CXXFLAGS="$CXXFLAGS -I./SeqAn-1.2"
++AM_CXXFLAGS="$CXXFLAGS -I/usr/include/seqan"
+ 
+ AC_SUBST(CC)
+ AC_SUBST(AM_CXXFLAGS)
diff --git a/debian/patches/series b/debian/patches/series
index e101519..a3d0eb4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+debian_seqan.patch
 fix_includes_path.patch
 bam2samtools

-- 
A spliced read mapper for RNA-Seq