academic/bcftools: Added (BCF calling tools).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 146 insertions, 0 deletions

diff --git a/academic/bcftools/README b/academic/bcftools/README
new file mode 100644
index 0000000000..731b912643
--- /dev/null
+++ b/academic/bcftools/README
@@ -0,0 +1,5 @@
+Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed in
+a single samtools-0.1.x package.
+This old version remains available from SBo as samtools-legacy
+
+The BCFtools is now distributed as an individual package.
diff --git a/academic/bcftools/bcftools.SlackBuild b/academic/bcftools/bcftools.SlackBuild
new file mode 100644
index 0000000000..5607ba9d9a
--- /dev/null
+++ b/academic/bcftools/bcftools.SlackBuild
@@ -0,0 +1,112 @@
+#!/bin/sh
+
+# Slackware build script for samtools
+
+# 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:
+#
+# 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=bcftools		
+VERSION=${VERSION:-1.9}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}	
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+    # Unless $ARCH is already set, use uname -m for all other archs:
+       *) ARCH=$( 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 $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2
+cd $PRGNAM-$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 {} \;
+
+#force linking to installed htslib
+rm -r htslib-$VERSION
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --with-htslib=system \
+  --enable-largefile \
+  --disable-configure-htslib \
+  --enable-bcftools-plugins \
+  --with-plugin-dir="/usr/libexec/${PRGNAM}" \
+  --with-plugin-path="/usr/libexec/${PRGNAM}" \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+
+make
+#make test
+make install DESTDIR=$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
+
+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 README LICENSE INSTALL NEWS \
+  $PKG/usr/doc/$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}
diff --git a/academic/bcftools/bcftools.info b/academic/bcftools/bcftools.info
new file mode 100644
index 0000000000..12d206a836
--- /dev/null
+++ b/academic/bcftools/bcftools.info
@@ -0,0 +1,10 @@
+PRGNAM="bcftools"
+VERSION="1.9"
+HOMEPAGE="http://www.htslib.org"
+DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2"
+MD5SUM="c8fb7bb9c9251342b0ecf1e6f0c98335"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="htslib"
+MAINTAINER="Rob van Nues"
+EMAIL="sborg63@disroot.org"
diff --git a/academic/bcftools/slack-desc b/academic/bcftools/slack-desc
new file mode 100644
index 0000000000..a5f72be8ed
--- /dev/null
+++ b/academic/bcftools/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+        |-----handy-ruler------------------------------------------------------|
+bcftools: bcftools (BCF calling tools)
+bcftools:
+bcftools: bcftools contains all the "vcf..." commands which previously lived in 
+bcftools: the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and 
+bcftools: the samtools BCF calling from bcftools subdirectory of the previous 
+bcftools: samtools. BCFtools are meant as a faster replacement for most of the 
+bcftools: perl VCFtools commands. Bcftools comes with its own hstlib sources.
+bcftools:
+bcftools: Home: http://www.htslib.org
+bcftools: 
+bcftools: