From 01f09cbeec562d978f78f636e1eeed9c0d6e50c8 Mon Sep 17 00:00:00 2001 From: Rob van Nues Date: Mon, 31 Dec 2018 08:30:54 +0700 Subject: academic/samtools: Updated for version 1.9 + new maintainer. Signed-off-by: Willy Sudiarto Raharjo --- academic/samtools/README | 29 +++------- academic/samtools/References | 5 -- academic/samtools/samtools.SlackBuild | 102 +++++++++++++++------------------- academic/samtools/samtools.info | 14 ++--- academic/samtools/slack-desc | 16 +++--- 5 files changed, 69 insertions(+), 97 deletions(-) delete mode 100644 academic/samtools/References (limited to 'academic') diff --git a/academic/samtools/README b/academic/samtools/README index 0203586f94..ea600cbe26 100644 --- a/academic/samtools/README +++ b/academic/samtools/README @@ -1,22 +1,11 @@ -SAM (Sequence Alignment/Map) format is a generic format for storing -large nucleotide sequence alignments. SAM aims to be a format that: +Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed +in a single samtools-0.1.x package. +This old version remains available from SBo as samtools-legacy -- Is flexible enough to store all the alignment information generated - by various alignment programs -- Is simple enough to be easily generated by alignment programs or - converted from existing alignment formats -- Is compact in file size -- Allows most of operations on the alignment to work on a stream - without loading the whole alignment into memory -- Allows the file to be indexed by genomic position to efficiently - retrieve all reads aligning to a locus. +Samtools is now distributed as an individual package. +Installation is set up so that the code uses an external HTSlib (also at SBo). +Although deprecated upstream, in the case that people need parts of samtools-legacy +(e.g header files or libbam) these can be installed from this package by modifying +the samtools.Slackbuild. -SAM Tools provide various utilities for manipulating alignments in the -SAM format, including sorting, merging, indexing and generating -alignments in a per-position format. - -Publication: -Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., -Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data -Processing Subgroup (2009) The Sequence alignment/map (SAM) format and -SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943] +Note that the sam.h of htslib differs from sam.h coming with samtools. diff --git a/academic/samtools/References b/academic/samtools/References deleted file mode 100644 index 1cc4af9500..0000000000 --- a/academic/samtools/References +++ /dev/null @@ -1,5 +0,0 @@ -Publication: -Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., -Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data -Processing Subgroup (2009) The Sequence alignment/map (SAM) format and -SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943] diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index 02dff9fbbe..daa7e87daf 100644 --- a/academic/samtools/samtools.SlackBuild +++ b/academic/samtools/samtools.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for samtools # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# All rights reserved. +# Copyright 2017-2018 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -22,17 +22,26 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# With help about the install paths from Arch Linux AUR: -# https://aur.archlinux.org/packages/sa/samtools/PKGBUILD - -PRGNAM=samtools -VERSION=${VERSION:-0.1.19} +PRGNAM=samtools +VERSION=${VERSION:-1.9} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +# Some applications still rely on the legacy samtools API instead of using htslib +# exclusively, in that case, install the headers in /usr/include/bam and the static +# libbam library as well by declaring (uncommenting): +#SAMLIB="yes" +# and commenting out: +SAMLIB="no" + +# WARNING: this package and htslib both provide a "sam.h" that aren't actually +# compatible with each other. Be extra careful about which file you're actually +# #including when using either of these packages for development work. + + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -43,8 +52,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -58,7 +67,6 @@ else fi set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -70,51 +78,23 @@ find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Use our CFLAGS/CXXFLAGS -sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile +# force linking to installed htslib +rm -r htslib-$VERSION CFLAGS="$SLKCFLAGS" \ -make -make razip - -# Install samtools, razip and bam library -install -D -m755 samtools $PKG/usr/bin/samtools -install -D -m755 razip $PKG/usr/bin/razip -install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/libbam.a - -# Install bcftools its library and vsfutils -cd bcftools -install -D -m755 bcftools $PKG/usr/bin/bcftools -install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a -install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils.pl - -# Include additional executables -cd ../misc -install -D -m755 ace2sam $PKG/usr/libexec/$PRGNAM/ace2sam -install -D -m755 bamcheck $PKG/usr/libexec/$PRGNAM/bamcheck -install -D -m755 maq2sam-long $PKG/usr/libexec/$PRGNAM/maq2sam-long -install -D -m755 maq2sam-short $PKG/usr/libexec/$PRGNAM/maq2sam-short -install -D -m755 md5fa $PKG/usr/libexec/$PRGNAM/md5fa -install -D -m755 md5sum-lite $PKG/usr/libexec/$PRGNAM/md5sum-lite -install -D -m755 wgsim $PKG/usr/libexec/$PRGNAM/wgsim - -# Include some scripts -mkdir -p $PKG/usr/share/$PRGNAM -cp -a \ - *.pl *.lua *.py plot-bamcheck \ - $PKG/usr/share/$PRGNAM +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --with-htslib=system \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux -# Include bam header files -cd .. -mkdir -p $PKG/usr/include/bam - for f in *.h ; do - install -m644 $f "$PKG/usr/include/bam" - done - -# Install manpage -install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 +make +make install DESTDIR=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -124,18 +104,26 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS COPYING INSTALL NEWS \ + AUTHORS LICENSE README INSTALL NEWS examples \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References -# Fix permissions in the package... -find $PKG/usr/{doc,include,share} \ --type d -exec chmod 755 {} \; -o \ --type f -exec chmod 644 {} \; +mkdir -p $PKG/usr/share/$PRGNAM-$VERSION + +cp -a \ + misc/*.lua \ + $PKG/usr/share/$PRGNAM-$VERSION mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +# include samtools-API if set above +if [ "$SAMLIB" = "yes" ] ; then + mkdir -p $PKG/usr/include/bam + mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} + install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}" + install -m644 *.h "$PKG/usr/include/bam" +fi + cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info index 79136533ae..1d724a44e4 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,10 +1,10 @@ PRGNAM="samtools" -VERSION="0.1.19" -HOMEPAGE="http://samtools.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2" -MD5SUM="ff8b46e6096cfb452003b1ec5091d86a" +VERSION="1.9" +HOMEPAGE="http://www.htslib.org" +DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2" +MD5SUM="cca9a40d9b91b007af2ff905cb8b5924" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" +REQUIRES="htslib" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/samtools/slack-desc b/academic/samtools/slack-desc index ce768600c2..8f1c434e47 100644 --- a/academic/samtools/slack-desc +++ b/academic/samtools/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| samtools: samtools (Sequence Alignment/Map Tools) samtools: -samtools: AM (Sequence Alignment/Map) format is a generic format for -samtools: storing large nucleotide sequence alignments. SAM Tools provide -samtools: various utilities for manipulating alignments in the SAM format, -samtools: including sorting, merging, indexing and generating alignments -samtools: in a per-position format. -samtools: -samtools: Home: http://samtools.sourceforge.net/ -samtools: References: /usr/doc/samtools-0.1.19/References +samtools: SAM (Sequence Alignment/Map) format is a generic format for +samtools: storing large nucleotide sequence alignments. The original samtools +samtools: package has been split into three separate but tightly coordinated +samtools: projects: htslib (C-library for handling high-throughput sequencing +samtools: data); samtools (for handling SAM, BAM, CRAM) and bcftools (for +samtools: handling VCF, BCF). Both samtools and bcftools are set up to use +samtools: system-wide installed hstlib sources. +samtools: Home: http://www.htslib.org samtools: -- cgit v1.2.3