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Diffstat (limited to 'academic/ncbi-blast/ncbi-blast.SlackBuild')
| -rw-r--r-- | academic/ncbi-blast/ncbi-blast.SlackBuild | 110 |
1 files changed, 110 insertions, 0 deletions
diff --git a/academic/ncbi-blast/ncbi-blast.SlackBuild b/academic/ncbi-blast/ncbi-blast.SlackBuild new file mode 100644 index 0000000000..34a7b03ac0 --- /dev/null +++ b/academic/ncbi-blast/ncbi-blast.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/sh + +# Slackware build script for ncbi-blast + +# 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=ncbi-blast +VERSION=${VERSION:-2.2.26} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=blast + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +# Determine the source arch +if [ "$ARCH" = "x86_64" ]; then + SRCARCH="x64" +else + SRCARCH="ia32" +fi + +# Construct the tarball name +TARNAME=$SRCNAM-$VERSION-$SRCARCH-linux + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$TARNAME.tar.gz +cd $SRCNAM-$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 {} \; + +# Install the precompiled binaries. Change the name of rpsblast, as it +# is also part of the ncbi-blast-plus package. +cd bin +install -D -m755 bl2seq $PKG/usr/bin/bl2seq +install -D -m755 blastall $PKG/usr/bin/blastall +install -D -m755 blastclust $PKG/usr/bin/blastclust +install -D -m755 blastpgp $PKG/usr/bin/blastpgp +install -D -m755 copymat $PKG/usr/bin/copymat +install -D -m755 fastacmd $PKG/usr/bin/fastacmd +install -D -m755 formatdb $PKG/usr/bin/formatdb +install -D -m755 formatrpsdb $PKG/usr/bin/formatrpsdb +install -D -m755 impala $PKG/usr/bin/impala +install -D -m755 makemat $PKG/usr/bin/makemat +install -D -m755 megablast $PKG/usr/bin/megablast +install -D -m755 rpsblast $PKG/usr/bin/rpsblast-legacy +install -D -m755 seedtop $PKG/usr/bin/seedtop +cd .. + +# Copy data dir +mkdir -p $PKG/usr/share/$PRGNAM +cp -a data $PKG/usr/share/$PRGNAM + +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 \ + doc/* VERSION \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +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} |