From 687759e7cdc6f178669b22721a26122d67e1fb6c Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 13 Jan 2013 10:23:45 +0100 Subject: academic/bowtie: Added (short read aligner of DNA sequences). Signed-off-by: Matteo Bernardini --- academic/bowtie/README | 17 +++++++ academic/bowtie/References | 5 ++ academic/bowtie/bowtie.SlackBuild | 104 ++++++++++++++++++++++++++++++++++++++ academic/bowtie/bowtie.info | 10 ++++ academic/bowtie/slack-desc | 19 +++++++ 5 files changed, 155 insertions(+) create mode 100644 academic/bowtie/README create mode 100644 academic/bowtie/References create mode 100644 academic/bowtie/bowtie.SlackBuild create mode 100644 academic/bowtie/bowtie.info create mode 100644 academic/bowtie/slack-desc (limited to 'academic') diff --git a/academic/bowtie/README b/academic/bowtie/README new file mode 100644 index 0000000000..949e67e5f8 --- /dev/null +++ b/academic/bowtie/README @@ -0,0 +1,17 @@ +Bowtie is an ultrafast, memory-efficient short read aligner geared +toward quickly aligning large sets of short DNA sequences (reads) to +large genomes. It aligns 35-base-pair reads to the human genome at a +rate of 25 million reads per hour on a typical workstation. Bowtie +indexes the genome with a Burrows-Wheeler index to keep its memory +footprint small: for the human genome, the index is typically about +2.2GB (for unpaired alignment) or 2.9GB (for paired-end or colorspace +alignment). Multiple processors can be used simultaneously to achieve +greater alignment speed. Bowtie can also output alignments in the +standard SAM format, allowing Bowtie to interoperate with other tools +supporting SAM, including the SAMtools consensus, SNP, and indel +callers. + +If you use Bowtie for your published research, please cite: +Langmead B, Trapnell C, Pop M, Salzberg SL. +Ultrafast and memory-efficient alignment of short DNA sequences to +the human genome. Genome Biol 10:R25. diff --git a/academic/bowtie/References b/academic/bowtie/References new file mode 100644 index 0000000000..43e42387ec --- /dev/null +++ b/academic/bowtie/References @@ -0,0 +1,5 @@ +If you use Bowtie for your published research, please cite: + +Langmead B, Trapnell C, Pop M, Salzberg SL. +Ultrafast and memory-efficient alignment of short DNA sequences to +the human genome. Genome Biol 10:R25. diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild new file mode 100644 index 0000000000..72eedc70ce --- /dev/null +++ b/academic/bowtie/bowtie.SlackBuild @@ -0,0 +1,104 @@ +#!/bin/sh + +# Slackware build script for bowtie + +# 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=bowtie +VERSION=${VERSION:-0.12.9} +BUILD=${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 +unzip $CWD/$PRGNAM-$VERSION-src.zip +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build +install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect + +# Copy genomic data, scripts and more +mkdir -p $PKG/usr/share/$PRGNAM +cp -a \ + genomes indexes reads scripts \ + $PKG/usr/share/$PRGNAM + +# Let's compress the E. coli genome and indexes +gzip $PKG/usr/share/$PRGNAM/genomes/*.fna +gzip $PKG/usr/share/$PRGNAM/indexes/*.ebwt + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS COPYING MANUAL NEWS TUTORIAL VERSION doc \ + $PKG/usr/doc/$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.${PKGTYPE:-tgz} diff --git a/academic/bowtie/bowtie.info b/academic/bowtie/bowtie.info new file mode 100644 index 0000000000..42f47f325f --- /dev/null +++ b/academic/bowtie/bowtie.info @@ -0,0 +1,10 @@ +PRGNAM="bowtie" +VERSION="0.12.9" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +DOWNLOAD="http://downloads.sourceforge.net/bowtie-bio/bowtie-0.12.9-src.zip" +MD5SUM="3120f57a849ab885e928800c591764f8" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/bowtie/slack-desc b/academic/bowtie/slack-desc new file mode 100644 index 0000000000..b1722ac279 --- /dev/null +++ b/academic/bowtie/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +bowtie: bowtie (A short read aligner of DNA sequences) +bowtie: +bowtie: Bowtie is an ultrafast, memory-efficient short read aligner geared +bowtie: toward quickly aligning large sets of short DNA sequences (reads) +bowtie: to large genomes. +bowtie: +bowtie: Home: http://bowtie-bio.sourceforge.net/ +bowtie: References: /usr/doc/bowtie-$VERSION/References +bowtie: +bowtie: +bowtie: -- cgit v1.2.3