From ab46533b5921c6b53b1bac23e99de90d20779895 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 13 Jan 2013 10:29:11 +0100 Subject: academic/bwa: Added (Burrows-Wheeler Aligner). Signed-off-by: Matteo Bernardini --- academic/bwa/README | 11 +++++ academic/bwa/References | 7 +++ academic/bwa/bwa.SlackBuild | 102 ++++++++++++++++++++++++++++++++++++++++++++ academic/bwa/bwa.info | 10 +++++ academic/bwa/slack-desc | 19 +++++++++ 5 files changed, 149 insertions(+) create mode 100644 academic/bwa/README create mode 100644 academic/bwa/References create mode 100644 academic/bwa/bwa.SlackBuild create mode 100644 academic/bwa/bwa.info create mode 100644 academic/bwa/slack-desc (limited to 'academic/bwa') diff --git a/academic/bwa/README b/academic/bwa/README new file mode 100644 index 0000000000..fe07da7e2d --- /dev/null +++ b/academic/bwa/README @@ -0,0 +1,11 @@ +Burrows-Wheeler Aligner (BWA) is an efficient program that aligns +relatively short nucleotide sequences against a long reference +sequence such as the human genome. It implements two algorithms, bwa- +short and BWA-SW. The former works for query sequences shorter than +200bp and the latter for longer sequences up to around 100kbp. Both +algorithms do gapped alignment. They are usually more accurate and +faster on queries with low error rates. + +If you use BWA-SW, please cite: +Li H. and Durbin R. (2010) Fast and accurate long-read alignment with +Burrows-Wheeler Transform. Bioinformatics, Epub. diff --git a/academic/bwa/References b/academic/bwa/References new file mode 100644 index 0000000000..e96223d8ec --- /dev/null +++ b/academic/bwa/References @@ -0,0 +1,7 @@ +The short read alignment component (bwa-short) has been published: +Li H. and Durbin R. (2009) Fast and accurate short read alignment +with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. + +If you use BWA-SW, please cite: +Li H. and Durbin R. (2010) Fast and accurate long-read alignment with +Burrows-Wheeler Transform. Bioinformatics, Epub. diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild new file mode 100644 index 0000000000..32d7e7d6a9 --- /dev/null +++ b/academic/bwa/bwa.SlackBuild @@ -0,0 +1,102 @@ +#!/bin/sh + +# Slackware build script for bwa + +# Copyright 2013 Petar Petrov, ppetrov@paju.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. + +PRGNAM=bwa +VERSION=${VERSION:-0.6.2} +BUILD=${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 . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# Use our CFLAGS/CXXFLAGS +sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile + +# This is needed for the build on 32bit system +sed -i "s:-DHAVE_PTHREAD #-D_NO_SSE2:-DHAVE_PTHREAD -D_NO_SSE2:" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +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 \ + ChangeLog COPYING README \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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.${PKGTYPE:-tgz} diff --git a/academic/bwa/bwa.info b/academic/bwa/bwa.info new file mode 100644 index 0000000000..0ef3c81947 --- /dev/null +++ b/academic/bwa/bwa.info @@ -0,0 +1,10 @@ +PRGNAM="bwa" +VERSION="0.6.2" +HOMEPAGE="http://bio-bwa.sourceforge.net/" +DOWNLOAD="http://downloads.sourceforge.net/bio-bwa/bwa-0.6.2.tar.bz2" +MD5SUM="5e4043769ce3436f6098ec67f6e02332" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/bwa/slack-desc b/academic/bwa/slack-desc new file mode 100644 index 0000000000..9d23eaa17c --- /dev/null +++ b/academic/bwa/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +bwa: bwa (Burrows-Wheeler Aligner) +bwa: +bwa: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns +bwa: relatively short nucleotide sequences against a long reference +bwa: sequence such as the human genome. It implements two algorithms, +bwa: bwa-short and BWA-SW. The former works for query sequences shorter +bwa: than 200bp and the latter for longer sequences up to around 100kbp. +bwa: +bwa: Home: http://bio-bwa.sourceforge.net/ +bwa: References: /usr/doc/bwa-$VERSION/References +bwa: -- cgit v1.2.3-65-gdbad