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author | Petar Petrov <ppetrov@paju.oulu.fi> | 2013-01-13 10:23:45 +0100 |
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committer | dsomero <xgizzmo@slackbuilds.org> | 2013-01-20 09:03:02 -0500 |
commit | 687759e7cdc6f178669b22721a26122d67e1fb6c (patch) | |
tree | b9d55209ca143fcf7739772ca1da68c75cb9cebb /academic/bowtie/bowtie.SlackBuild | |
parent | fb948c0ed12cda15f62d076b255068a7f8c4e36a (diff) | |
download | slackbuilds-687759e7cdc6f178669b22721a26122d67e1fb6c.tar.gz |
academic/bowtie: Added (short read aligner of DNA sequences).
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
Diffstat (limited to 'academic/bowtie/bowtie.SlackBuild')
-rw-r--r-- | academic/bowtie/bowtie.SlackBuild | 104 |
1 files changed, 104 insertions, 0 deletions
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} |