diff options
Diffstat (limited to 'academic/samtools-legacy/samtools-legacy.SlackBuild')
| -rw-r--r-- | academic/samtools-legacy/samtools-legacy.SlackBuild | 143 |
1 files changed, 143 insertions, 0 deletions
diff --git a/academic/samtools-legacy/samtools-legacy.SlackBuild b/academic/samtools-legacy/samtools-legacy.SlackBuild new file mode 100644 index 0000000000..ca6af2ff5a --- /dev/null +++ b/academic/samtools-legacy/samtools-legacy.SlackBuild @@ -0,0 +1,143 @@ +#!/bin/sh + +# Slackware build script for samtools-legacy + +# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# 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. + +# With help about the install paths from Arch Linux AUR: +# https://aur.archlinux.org/packages/sa/samtools/PKGBUILD + +SRCNAM=samtools +SUFFIX=legacy +PRGNAM=${SRCNAM}-${SUFFIX} +VERSION=${VERSION:-0.1.19} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -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 $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.bz2 +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Use our CFLAGS/CXXFLAGS +sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +make +make razip + +# Install samtools, razip and bam library +install -D -m755 samtools $PKG/usr/bin/samtools-$SUFFIX +install -D -m755 razip $PKG/usr/bin/razip-$SUFFIX +install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/libbam.a + +# Install bcftools its library and vsfutils +cd bcftools +install -D -m755 bcftools $PKG/usr/bin/bcftools-$SUFFIX +install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/$PRGNAM/libbcf.a +install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils-$SUFFIX.pl + +# Include additional executables +cd ../misc +install -D -m755 ace2sam $PKG/usr/libexec/$PRGNAM/ace2sam +install -D -m755 bamcheck $PKG/usr/libexec/$PRGNAM/bamcheck +install -D -m755 maq2sam-long $PKG/usr/libexec/$PRGNAM/maq2sam-long +install -D -m755 maq2sam-short $PKG/usr/libexec/$PRGNAM/maq2sam-short +install -D -m755 md5fa $PKG/usr/libexec/$PRGNAM/md5fa +install -D -m755 md5sum-lite $PKG/usr/libexec/$PRGNAM/md5sum-lite +install -D -m755 wgsim $PKG/usr/libexec/$PRGNAM/wgsim + +# Include some scripts +mkdir -p $PKG/usr/share/$PRGNAM +cp -a \ + *.pl *.lua *.py plot-bamcheck \ + $PKG/usr/share/$PRGNAM + +# Include bam header files +cd .. +mkdir -p $PKG/usr/include/bam-$SUFFIX + for f in *.h ; do + install -m644 $f "$PKG/usr/include/bam-$SUFFIX" + done + +# Install manpage +install -D -m644 $SRCNAM.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 \ + AUTHORS COPYING INSTALL NEWS \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +# Fix permissions in the package... +find $PKG/usr/{doc,include,share} \ +-type d -exec chmod 755 {} \; -o \ +-type f -exec chmod 644 {} \; + +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} |