diff options
Diffstat (limited to 'academic/samtools/samtools.SlackBuild')
| -rw-r--r-- | academic/samtools/samtools.SlackBuild | 102 |
1 files changed, 45 insertions, 57 deletions
diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index 02dff9fbbe..daa7e87daf 100644 --- a/academic/samtools/samtools.SlackBuild +++ b/academic/samtools/samtools.SlackBuild @@ -3,7 +3,7 @@ # Slackware build script for samtools # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# All rights reserved. +# Copyright 2017-2018 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: @@ -22,17 +22,26 @@ # 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 - -PRGNAM=samtools -VERSION=${VERSION:-0.1.19} +PRGNAM=samtools +VERSION=${VERSION:-1.9} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +# Some applications still rely on the legacy samtools API instead of using htslib +# exclusively, in that case, install the headers in /usr/include/bam and the static +# libbam library as well by declaring (uncommenting): +#SAMLIB="yes" +# and commenting out: +SAMLIB="no" + +# WARNING: this package and htslib both provide a "sam.h" that aren't actually +# compatible with each other. Be extra careful about which file you're actually +# #including when using either of these packages for development work. + + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -43,8 +52,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -58,7 +67,6 @@ else fi set -e - rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP @@ -70,51 +78,23 @@ 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 {} \; + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Use our CFLAGS/CXXFLAGS -sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile +# force linking to installed htslib +rm -r htslib-$VERSION CFLAGS="$SLKCFLAGS" \ -make -make razip - -# Install samtools, razip and bam library -install -D -m755 samtools $PKG/usr/bin/samtools -install -D -m755 razip $PKG/usr/bin/razip -install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/libbam.a - -# Install bcftools its library and vsfutils -cd bcftools -install -D -m755 bcftools $PKG/usr/bin/bcftools -install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a -install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils.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 +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --with-htslib=system \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux -# Include bam header files -cd .. -mkdir -p $PKG/usr/include/bam - for f in *.h ; do - install -m644 $f "$PKG/usr/include/bam" - done - -# Install manpage -install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 +make +make install DESTDIR=$PKG 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 @@ -124,18 +104,26 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS COPYING INSTALL NEWS \ + AUTHORS LICENSE README INSTALL NEWS examples \ $PKG/usr/doc/$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 $PKG/usr/share/$PRGNAM-$VERSION + +cp -a \ + misc/*.lua \ + $PKG/usr/share/$PRGNAM-$VERSION mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +# include samtools-API if set above +if [ "$SAMLIB" = "yes" ] ; then + mkdir -p $PKG/usr/include/bam + mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} + install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}" + install -m644 *.h "$PKG/usr/include/bam" +fi + cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} |