diff options
Diffstat (limited to 'academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild')
| -rw-r--r-- | academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild | 115 |
1 files changed, 115 insertions, 0 deletions
diff --git a/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild b/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild new file mode 100644 index 0000000000000..c3a677bdadaaf --- /dev/null +++ b/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild @@ -0,0 +1,115 @@ +#!/bin/sh + +# Slackware build script for ncbi-blast-plus + +# 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-plus +VERSION=${VERSION:-2.2.27} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=ncbi-blast +SRCVER=2.2.27+ + +if [ -z "$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-$SRCVER-$SRCARCH-linux + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$TARNAME.tar.gz +cd $SRCNAM-$SRCVER +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. +cd bin +install -D -m755 blast_formatter $PKG/usr/bin/blast_formatter +install -D -m755 blastdb_aliastool $PKG/usr/bin/blastdb_aliastool +install -D -m755 blastdbcheck $PKG/usr/bin/blastdbcheck +install -D -m755 blastdbcmd $PKG/usr/bin/blastdbcmd +install -D -m755 blastn $PKG/usr/bin/blastn +install -D -m755 blastp $PKG/usr/bin/blastp +install -D -m755 blastx $PKG/usr/bin/blastx +install -D -m755 convert2blastmask $PKG/usr/bin/convert2blastmask +install -D -m755 deltablast $PKG/usr/bin/deltablast +install -D -m755 dustmasker $PKG/usr/bin/dustmasker +install -D -m755 legacy_blast.pl $PKG/usr/bin/legacy_blast.pl +install -D -m755 makeblastdb $PKG/usr/bin/makeblastdb +install -D -m755 makembindex $PKG/usr/bin/makembindex +install -D -m755 makeprofiledb $PKG/usr/bin/makeprofiledb +install -D -m755 psiblast $PKG/usr/bin/psiblast +install -D -m755 rpsblast $PKG/usr/bin/rpsblast +install -D -m755 rpstblastn $PKG/usr/bin/rpstblastn +install -D -m755 segmasker $PKG/usr/bin/segmasker +install -D -m755 tblastn $PKG/usr/bin/tblastn +install -D -m755 tblastx $PKG/usr/bin/tblastx +install -D -m755 update_blastdb.pl $PKG/usr/bin/update_blastdb.pl +install -D -m755 windowmasker $PKG/usr/bin/windowmasker +cd .. + +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 \ + ChangeLog LICENSE README \ + $PKG/usr/doc/$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} |