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academic/samtools-legacy: Added (Sequence Alignment/Map Tools).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
c0f0a1270e
commit
9180142c4c
5 changed files with 205 additions and 0 deletions
28
academic/samtools-legacy/README
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28
academic/samtools-legacy/README
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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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- 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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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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NOTE!
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This is an older version of the program, kept here for compatibility
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with Ugene. You can safely install it along the new one. When you start
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Ugene, go to Settings > Preferences > External Tools and manually select
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the legacy binaries in /usr/bin/
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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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5
academic/samtools-legacy/References
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5
academic/samtools-legacy/References
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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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143
academic/samtools-legacy/samtools-legacy.SlackBuild
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143
academic/samtools-legacy/samtools-legacy.SlackBuild
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#!/bin/sh
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# Slackware build script for samtools-legacy
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# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com
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# 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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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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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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SRCNAM=samtools
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SUFFIX=legacy
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PRGNAM=${SRCNAM}-${SUFFIX}
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VERSION=${VERSION:-0.1.19}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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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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rm -rf $SRCNAM-$VERSION
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tar xvf $CWD/$SRCNAM-$VERSION.tar.bz2
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cd $SRCNAM-$VERSION
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chown -R root:root .
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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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# Use our CFLAGS/CXXFLAGS
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sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
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CFLAGS="$SLKCFLAGS" \
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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 $PKG/usr/bin/samtools-$SUFFIX
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install -D -m755 razip $PKG/usr/bin/razip-$SUFFIX
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install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/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 $PKG/usr/bin/bcftools-$SUFFIX
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install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/libbcf.a
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install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils-$SUFFIX.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 $PKG/usr/include/bam-$SUFFIX
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for f in *.h ; do
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install -m644 $f "$PKG/usr/include/bam-$SUFFIX"
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done
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# Install manpage
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install -D -m644 $SRCNAM.1 $PKG/usr/man/man1/$PRGNAM.1
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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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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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AUTHORS COPYING INSTALL NEWS \
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$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/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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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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10
academic/samtools-legacy/samtools-legacy.info
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10
academic/samtools-legacy/samtools-legacy.info
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PRGNAM="samtools-legacy"
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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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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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19
academic/samtools-legacy/slack-desc
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19
academic/samtools-legacy/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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samtools-legacy: samtools-legacy (Sequence Alignment/Map Tools version 0.1.19)
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samtools-legacy:
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samtools-legacy: AM (Sequence Alignment/Map) format is a generic format for
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samtools-legacy: storing large nucleotide sequence alignments. SAM Tools provide
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samtools-legacy: various utilities for manipulating alignments in the SAM format,
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samtools-legacy: including sorting, merging, indexing and generating alignments
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samtools-legacy: in a per-position format.
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samtools-legacy:
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samtools-legacy: Home: http://samtools.sourceforge.net/
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samtools-legacy: References: /usr/doc/samtools-0.1.19/References
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samtools-legacy:
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