gentoo-overlay/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch

Description: Use Debian packaged SeqAn library instead of copy in upstream source
Author: Andreas Tille <tille@debian.org>
Date: 2011-01-30
Last-Update: 2013-04-18
Reviewed-by: Ognyan Kulev <ogi@debian.org>

--- a/Makefile
+++ b/Makefile
@@ -5,9 +5,7 @@
 prefix = /usr/local
 bindir = $(prefix)/bin
 
-SEQAN_DIR = SeqAn-1.1
-SEQAN_INC = -I $(SEQAN_DIR)
-INC = $(SEQAN_INC) -I third_party
+INC = `pkg-config --cflags seqan-1.4`
 CPP = g++
 CXX = $(CPP)
 CC = gcc
@@ -168,7 +166,6 @@
                $(wildcard genomes/NC_008253.fna) \
                $(wildcard reads/e_coli_1000.*) \
                $(wildcard reads/e_coli_1000_*) \
-               SeqAn-1.1 \
                bowtie \
                bowtie-build \
                bowtie-inspect \