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academic/bowtie: Updated for version 1.0.0.

Browse source 
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov 2013-12-14 07:31:21 +07:00 committed by Erik Hanson
parent ca3a131931
commit 7001301775
7 changed files with 118 additions and 13 deletions
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22
academic/bowtie/bowtie.SlackBuild
View file

@ -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

8
academic/bowtie/bowtie.info
View file

@ -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"

20
academic/bowtie/patches/disable_bits_flag.patch Normal file
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@ -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

20
academic/bowtie/patches/no_hash_style_both_for_mips.patch Normal file
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@ -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 =

42
academic/bowtie/patches/seqan-fix-setBegin-call.patch Normal file
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@ -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);
}
}

17
academic/bowtie/patches/use-dpkg-buildflags.patch Normal file
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@ -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)\""

2
academic/bowtie/slack-desc
View file

@ -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: