From cc1fa6dad0a542868d3db4dd8c529dc19f7626c8 Mon Sep 17 00:00:00 2001 From: Rob van Nues Date: Mon, 31 Dec 2018 08:24:27 +0700 Subject: academic/bcftools: Added (BCF calling tools). Signed-off-by: Willy Sudiarto Raharjo --- academic/bcftools/README | 5 ++ academic/bcftools/bcftools.SlackBuild | 112 ++++++++++++++++++++++++++++++++++ academic/bcftools/bcftools.info | 10 +++ academic/bcftools/slack-desc | 19 ++++++ 4 files changed, 146 insertions(+) create mode 100644 academic/bcftools/README create mode 100644 academic/bcftools/bcftools.SlackBuild create mode 100644 academic/bcftools/bcftools.info create mode 100644 academic/bcftools/slack-desc (limited to 'academic') 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: -- cgit v1.2.3