academic/bowtie: Updated for version 1.0.0.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

7 files changed, 118 insertions, 13 deletions

diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild
index a4b3ce38e6..cb9ab8a4fc 100644
--- a/academic/bowtie/bowtie.SlackBuild
+++ b/academic/bowtie/bowtie.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for bowtie
 
-# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=bowtie
-VERSION=${VERSION:-0.12.9}
+VERSION=${VERSION:-1.0.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -60,14 +60,20 @@ rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
 rm -rf $PRGNAM-$VERSION
-unzip $CWD/$PRGNAM-$VERSION-src.zip
+tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz
 cd $PRGNAM-$VERSION
 chown -R root:root .
 find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# Thanks to Debian for the set of patches!
+patch -p1 -i $CWD/patches/disable_bits_flag.patch
+patch -p1 -i $CWD/patches/no_hash_style_both_for_mips.patch
+patch -p1 -i $CWD/patches/seqan-fix-setBegin-call.patch
+patch -p1 -i $CWD/patches/use-dpkg-buildflags.patch
 
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
@@ -92,7 +98,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  AUTHORS COPYING MANUAL NEWS TUTORIAL VERSION doc \
+  AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
diff --git a/academic/bowtie/bowtie.info b/academic/bowtie/bowtie.info
index 42f47f325f..81e5ecbd0b 100644
--- a/academic/bowtie/bowtie.info
+++ b/academic/bowtie/bowtie.info
@@ -1,10 +1,10 @@
 PRGNAM="bowtie"
-VERSION="0.12.9"
+VERSION="1.0.0"
 HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-DOWNLOAD="http://downloads.sourceforge.net/bowtie-bio/bowtie-0.12.9-src.zip"
-MD5SUM="3120f57a849ab885e928800c591764f8"
+DOWNLOAD="http://ftp.de.debian.org/debian/pool/main/b/bowtie/bowtie_1.0.0.orig.tar.gz"
+MD5SUM="75d402c856b64958ec4bc0f67d011eb9"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
 MAINTAINER="Petar Petrov"
-EMAIL="ppetrov@paju.oulu.fi"
+EMAIL="petar.petrov@student.oulu.fi"
diff --git a/academic/bowtie/patches/disable_bits_flag.patch b/academic/bowtie/patches/disable_bits_flag.patch
new file mode 100644
index 0000000000..3d849240e7
--- /dev/null
+++ b/academic/bowtie/patches/disable_bits_flag.patch
@@ -0,0 +1,20 @@
+Description: Disable architecture bits detection.
+ In Debian, you can use multiarch facilities for choosing which version 
+ to run.
+Author: Ognyan Kulev <ogi@debian.org>
+Forwarded: not-needed 
+Last-Update: 2013-04-24 
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bowtie-1.0.0.orig/Makefile
++++ bowtie-1.0.0/Makefile
+@@ -121,6 +121,9 @@
+     BITS_FLAG = -m64
+ endif
+ 
++# Debian: Disable selection of 32/64-bits. Use multiarch instead.
++BITS_FLAG =
++
+ DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
+ RELEASE_FLAGS = -O3 $(BITS_FLAG)
+ NOASSERT_FLAGS = -DNDEBUG
diff --git a/academic/bowtie/patches/no_hash_style_both_for_mips.patch b/academic/bowtie/patches/no_hash_style_both_for_mips.patch
new file mode 100644
index 0000000000..c7f8ab32e1
--- /dev/null
+++ b/academic/bowtie/patches/no_hash_style_both_for_mips.patch
@@ -0,0 +1,20 @@
+Description: Disable -Wl,--hash-style=both on mips machines.
+ It's not supported on mips and mipsel ports and leads to build errors.
+Author: Ognyan Kulev <ogi@debian.org>
+Forwarded: not-needed
+Last-Update: 2013-04-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bowtie-1.0.0.orig/Makefile
++++ bowtie-1.0.0/Makefile
+@@ -45,7 +45,9 @@
+ LINUX = 0
+ ifneq (,$(findstring Linux,$(shell uname)))
+     LINUX = 1
+-    EXTRA_FLAGS += -Wl,--hash-style=both
++    ifeq (,$(findstring mips,$(shell uname -m)))
++        EXTRA_FLAGS += -Wl,--hash-style=both
++    endif
+ endif
+ 
+ MM_DEF = 
diff --git a/academic/bowtie/patches/seqan-fix-setBegin-call.patch b/academic/bowtie/patches/seqan-fix-setBegin-call.patch
new file mode 100644
index 0000000000..56c8763117
--- /dev/null
+++ b/academic/bowtie/patches/seqan-fix-setBegin-call.patch
@@ -0,0 +1,42 @@
+Description: Proper type-casting in using seqan::_setBegin().
+ Required by newer versions of GCC.
+Forwarded: no
+Author: Ognyan Kulev <ogi@debian.org>
+Last-Update: 2013-04-18
+
+--- a/pat.h
++++ b/pat.h
+@@ -82,20 +82,20 @@
+ 	~ReadBuf() {
+ 		clearAll(); reset();
+ 		// Prevent seqan from trying to free buffers
+-		_setBegin(patFw, NULL);
+-		_setBegin(patRc, NULL);
+-		_setBegin(qual, NULL);
+-		_setBegin(patFwRev, NULL);
+-		_setBegin(patRcRev, NULL);
+-		_setBegin(qualRev, NULL);
+-		_setBegin(name, NULL);
++		_setBegin(patFw, (Dna5*)NULL);
++		_setBegin(patRc, (Dna5*)NULL);
++		_setBegin(qual, (char*)NULL);
++		_setBegin(patFwRev, (Dna5*)NULL);
++		_setBegin(patRcRev, (Dna5*)NULL);
++		_setBegin(qualRev, (char*)NULL);
++		_setBegin(name, (char*)NULL);
+ 		for(int j = 0; j < 3; j++) {
+-			_setBegin(altPatFw[j], NULL);
+-			_setBegin(altPatFwRev[j], NULL);
+-			_setBegin(altPatRc[j], NULL);
+-			_setBegin(altPatRcRev[j], NULL);
+-			_setBegin(altQual[j], NULL);
+-			_setBegin(altQualRev[j], NULL);
++			_setBegin(altPatFw[j], (Dna5*)NULL);
++			_setBegin(altPatFwRev[j], (Dna5*)NULL);
++			_setBegin(altPatRc[j], (Dna5*)NULL);
++			_setBegin(altPatRcRev[j], (Dna5*)NULL);
++			_setBegin(altQual[j], (char*)NULL);
++			_setBegin(altQualRev[j], (char*)NULL);
+ 		}
+ 	}
+ 
diff --git a/academic/bowtie/patches/use-dpkg-buildflags.patch b/academic/bowtie/patches/use-dpkg-buildflags.patch
new file mode 100644
index 0000000000..7225d19af2
--- /dev/null
+++ b/academic/bowtie/patches/use-dpkg-buildflags.patch
@@ -0,0 +1,17 @@
+Description: Use build flags from environment (dpkg-buildflags).
+ Necessary for hardening flags.
+Author: Simon Ruderich <simon@ruderich.org>
+Last-Update: 2012-04-24
+Bug-Closed: http://bugs.debian.org/670230
+
+--- a/Makefile
++++ b/Makefile
+@@ -173,7 +173,7 @@
+      $(MM_DEF) \
+      $(SHMEM_DEF)
+ 
+-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
++ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
+ RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
+ 
diff --git a/academic/bowtie/slack-desc b/academic/bowtie/slack-desc
index b1722ac279..989d20d4e2 100644
--- a/academic/bowtie/slack-desc
+++ b/academic/bowtie/slack-desc
@@ -13,7 +13,7 @@ bowtie: toward quickly aligning large sets of short DNA sequences (reads)
 bowtie: to large genomes.
 bowtie:
 bowtie: Home: http://bowtie-bio.sourceforge.net/
-bowtie: References: /usr/doc/bowtie-$VERSION/References
+bowtie: References: /usr/doc/bowtie-1.0.0/References
 bowtie:
 bowtie:
 bowtie: