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academic/samtools: Updated for version 1.9 + new maintainer.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Rob van Nues
Willy Sudiarto Raharjo
parent
cc1fa6dad0
commit
01f09cbeec
5 changed files with 69 additions and 97 deletions
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@ -1,22 +1,11 @@
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SAM (Sequence Alignment/Map) format is a generic format for storing
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large nucleotide sequence alignments. SAM aims to be a format that:
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Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed
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in a single samtools-0.1.x package.
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This old version remains available from SBo as samtools-legacy
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- Is flexible enough to store all the alignment information generated
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by various alignment programs
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- Is simple enough to be easily generated by alignment programs or
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converted from existing alignment formats
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- Is compact in file size
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- Allows most of operations on the alignment to work on a stream
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without loading the whole alignment into memory
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- Allows the file to be indexed by genomic position to efficiently
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retrieve all reads aligning to a locus.
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Samtools is now distributed as an individual package.
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Installation is set up so that the code uses an external HTSlib (also at SBo).
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Although deprecated upstream, in the case that people need parts of samtools-legacy
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(e.g header files or libbam) these can be installed from this package by modifying
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the samtools.Slackbuild.
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SAM Tools provide various utilities for manipulating alignments in the
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SAM format, including sorting, merging, indexing and generating
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alignments in a per-position format.
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Publication:
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Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
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Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
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Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
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SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
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Note that the sam.h of htslib differs from sam.h coming with samtools.
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@ -1,5 +0,0 @@
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Publication:
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Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
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Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
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Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
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SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
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@ -3,7 +3,7 @@
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# Slackware build script for samtools
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# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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# Copyright 2017-2018 Rob van Nues # All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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@ -22,17 +22,26 @@
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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# With help about the install paths from Arch Linux AUR:
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# https://aur.archlinux.org/packages/sa/samtools/PKGBUILD
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PRGNAM=samtools
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VERSION=${VERSION:-0.1.19}
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PRGNAM=samtools
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VERSION=${VERSION:-1.9}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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# Some applications still rely on the legacy samtools API instead of using htslib
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# exclusively, in that case, install the headers in /usr/include/bam and the static
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# libbam library as well by declaring (uncommenting):
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#SAMLIB="yes"
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# and commenting out:
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SAMLIB="no"
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# WARNING: this package and htslib both provide a "sam.h" that aren't actually
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# compatible with each other. Be extra careful about which file you're actually
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# #including when using either of these packages for development work.
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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@ -43,8 +52,8 @@ TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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@ -58,7 +67,6 @@ else
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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@ -70,51 +78,23 @@ find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Use our CFLAGS/CXXFLAGS
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sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
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# force linking to installed htslib
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rm -r htslib-$VERSION
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib${LIBDIRSUFFIX} \
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--with-htslib=system \
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--mandir=/usr/man \
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--docdir=/usr/doc/$PRGNAM-$VERSION \
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--build=$ARCH-slackware-linux
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make
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make razip
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# Install samtools, razip and bam library
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install -D -m755 samtools $PKG/usr/bin/samtools
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install -D -m755 razip $PKG/usr/bin/razip
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install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/libbam.a
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# Install bcftools its library and vsfutils
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cd bcftools
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install -D -m755 bcftools $PKG/usr/bin/bcftools
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install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a
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install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils.pl
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# Include additional executables
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cd ../misc
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install -D -m755 ace2sam $PKG/usr/libexec/$PRGNAM/ace2sam
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install -D -m755 bamcheck $PKG/usr/libexec/$PRGNAM/bamcheck
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install -D -m755 maq2sam-long $PKG/usr/libexec/$PRGNAM/maq2sam-long
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install -D -m755 maq2sam-short $PKG/usr/libexec/$PRGNAM/maq2sam-short
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install -D -m755 md5fa $PKG/usr/libexec/$PRGNAM/md5fa
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install -D -m755 md5sum-lite $PKG/usr/libexec/$PRGNAM/md5sum-lite
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install -D -m755 wgsim $PKG/usr/libexec/$PRGNAM/wgsim
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# Include some scripts
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a \
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*.pl *.lua *.py plot-bamcheck \
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$PKG/usr/share/$PRGNAM
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# Include bam header files
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cd ..
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mkdir -p $PKG/usr/include/bam
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for f in *.h ; do
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install -m644 $f "$PKG/usr/include/bam"
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done
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# Install manpage
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install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
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make install DESTDIR=$PKG
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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@ -124,18 +104,26 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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AUTHORS COPYING INSTALL NEWS \
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AUTHORS LICENSE README INSTALL NEWS examples \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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# Fix permissions in the package...
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find $PKG/usr/{doc,include,share} \
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-type d -exec chmod 755 {} \; -o \
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-type f -exec chmod 644 {} \;
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mkdir -p $PKG/usr/share/$PRGNAM-$VERSION
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cp -a \
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misc/*.lua \
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$PKG/usr/share/$PRGNAM-$VERSION
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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# include samtools-API if set above
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if [ "$SAMLIB" = "yes" ] ; then
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mkdir -p $PKG/usr/include/bam
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mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
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install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
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install -m644 *.h "$PKG/usr/include/bam"
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fi
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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@ -1,10 +1,10 @@
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PRGNAM="samtools"
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VERSION="0.1.19"
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HOMEPAGE="http://samtools.sourceforge.net/"
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DOWNLOAD="http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2"
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MD5SUM="ff8b46e6096cfb452003b1ec5091d86a"
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VERSION="1.9"
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HOMEPAGE="http://www.htslib.org"
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DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2"
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MD5SUM="cca9a40d9b91b007af2ff905cb8b5924"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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REQUIRES="htslib"
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MAINTAINER="Rob van Nues"
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EMAIL="sborg63@disroot.org"
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@ -8,12 +8,12 @@
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|-----handy-ruler------------------------------------------------------|
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samtools: samtools (Sequence Alignment/Map Tools)
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samtools:
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samtools: AM (Sequence Alignment/Map) format is a generic format for
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samtools: storing large nucleotide sequence alignments. SAM Tools provide
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samtools: various utilities for manipulating alignments in the SAM format,
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samtools: including sorting, merging, indexing and generating alignments
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samtools: in a per-position format.
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samtools:
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samtools: Home: http://samtools.sourceforge.net/
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samtools: References: /usr/doc/samtools-0.1.19/References
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samtools: SAM (Sequence Alignment/Map) format is a generic format for
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samtools: storing large nucleotide sequence alignments. The original samtools
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samtools: package has been split into three separate but tightly coordinated
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samtools: projects: htslib (C-library for handling high-throughput sequencing
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samtools: data); samtools (for handling SAM, BAM, CRAM) and bcftools (for
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samtools: handling VCF, BCF). Both samtools and bcftools are set up to use
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samtools: system-wide installed hstlib sources.
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samtools: Home: http://www.htslib.org
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samtools:
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