diff options
| -rw-r--r-- | academic/bowtie/bowtie.SlackBuild | 22 | ||||
| -rw-r--r-- | academic/bowtie/bowtie.info | 8 | ||||
| -rw-r--r-- | academic/bowtie/patches/disable_bits_flag.patch | 20 | ||||
| -rw-r--r-- | academic/bowtie/patches/no_hash_style_both_for_mips.patch | 20 | ||||
| -rw-r--r-- | academic/bowtie/patches/seqan-fix-setBegin-call.patch | 42 | ||||
| -rw-r--r-- | academic/bowtie/patches/use-dpkg-buildflags.patch | 17 | ||||
| -rw-r--r-- | academic/bowtie/slack-desc | 2 |
7 files changed, 118 insertions, 13 deletions
diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild index a4b3ce38e64ad..cb9ab8a4fc6d5 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 42f47f325fda8..81e5ecbd0b536 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 0000000000000..3d849240e7b28 --- /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 $(BITS_FLAG) + NOASSERT_FLAGS = -DNDEBUG diff --git a/academic/bowtie/patches/no_hash_style_both_for_mips.patch b/academic/bowtie/patches/no_hash_style_both_for_mips.patch new file mode 100644 index 0000000000000..c7f8ab32e1462 --- /dev/null +++ b/academic/bowtie/patches/no_hash_style_both_for_mips.patch @@ -0,0 +1,20 @@ +Description: Disable -Wl,--hash-style=both on mips machines. + It's not supported on mips and mipsel ports and leads to build errors. +Author: Ognyan Kulev <ogi@debian.org> +Forwarded: not-needed +Last-Update: 2013-04-24 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bowtie-1.0.0.orig/Makefile ++++ bowtie-1.0.0/Makefile +@@ -45,7 +45,9 @@ + LINUX = 0 + ifneq (,$(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 0000000000000..56c8763117c90 --- /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 0000000000000..7225d19af2c2d --- /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) $(ALL_FLAGS)\"" + diff --git a/academic/bowtie/slack-desc b/academic/bowtie/slack-desc index b1722ac279c39..989d20d4e28cd 100644 --- a/academic/bowtie/slack-desc +++ b/academic/bowtie/slack-desc @@ -13,7 +13,7 @@ bowtie: toward quickly aligning large sets of short DNA sequences (reads) bowtie: to large genomes. bowtie: bowtie: Home: http://bowtie-bio.sourceforge.net/ -bowtie: References: /usr/doc/bowtie-$VERSION/References +bowtie: References: /usr/doc/bowtie-1.0.0/References bowtie: bowtie: bowtie: |