diff options
author | Petar Petrov <petar.petrov@student.oulu.fi> | 2013-12-14 08:02:52 +0700 |
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committer | Erik Hanson <erik@slackbuilds.org> | 2013-12-14 10:53:05 -0600 |
commit | 00017f6260e9e0d2951eac42aeea9d8fbb9f1034 (patch) | |
tree | ed8db6c055c2fc57e4f322ececdf77392e77c6d3 /academic/samtools | |
parent | 723d17ef4fdabd19a8004eb40ec1864d78082c8c (diff) |
academic/samtools: Added (Sequence Alignment/Map Tools).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/samtools')
-rw-r--r-- | academic/samtools/README | 22 | ||||
-rw-r--r-- | academic/samtools/References | 5 | ||||
-rw-r--r-- | academic/samtools/samtools.SlackBuild | 141 | ||||
-rw-r--r-- | academic/samtools/samtools.info | 10 | ||||
-rw-r--r-- | academic/samtools/slack-desc | 19 |
5 files changed, 197 insertions, 0 deletions
diff --git a/academic/samtools/README b/academic/samtools/README new file mode 100644 index 0000000000000..0203586f94268 --- /dev/null +++ b/academic/samtools/README @@ -0,0 +1,22 @@ +SAM (Sequence Alignment/Map) format is a generic format for storing +large nucleotide sequence alignments. SAM aims to be a format that: + +- 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. + +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] diff --git a/academic/samtools/References b/academic/samtools/References new file mode 100644 index 0000000000000..1cc4af9500b22 --- /dev/null +++ b/academic/samtools/References @@ -0,0 +1,5 @@ +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 new file mode 100644 index 0000000000000..a3c0e2d1a7d5a --- /dev/null +++ b/academic/samtools/samtools.SlackBuild @@ -0,0 +1,141 @@ +#!/bin/sh + +# Slackware build script for samtools + +# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# 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=${VERSION:-0.1.19} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 +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 \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Use our CFLAGS/CXXFLAGS +sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile + +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 + +# 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 + +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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS COPYING INSTALL NEWS \ + $PKG/usr/doc/$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/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +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 new file mode 100644 index 0000000000000..51a89dca1e0e7 --- /dev/null +++ b/academic/samtools/samtools.info @@ -0,0 +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" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/samtools/slack-desc b/academic/samtools/slack-desc new file mode 100644 index 0000000000000..ce768600c2978 --- /dev/null +++ b/academic/samtools/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----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: |