academic/vcftools: Added (A program designed for working with VCF).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Erik Hanson
parent
ae708391b5
commit
2ac6480638
|
|
@ -0,0 +1,18 @@
|
|||
VCFtools is a program package designed for working with VCF files,
|
||||
such as those generated by the 1000 Genomes Project. The aim of
|
||||
VCFtools is to provide methods for working with VCF files: validating,
|
||||
merging, comparing and calculate some basic population genetic
|
||||
statistics.
|
||||
|
||||
VCFtools supports the VCF format v4.0. The vcf-validator, Perl API and
|
||||
scripts now support also VCF format v4.2 and maintain backward
|
||||
compatibility with older versions.
|
||||
|
||||
If you make use of VCFtools in your research, the authors would
|
||||
appreciate a citation of the following paper:
|
||||
|
||||
The Variant Call Format and VCFtools,
|
||||
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers,
|
||||
Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter,
|
||||
Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin
|
||||
and 1000 Genomes Project Analysis Group, Bioinformatics, 2011
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
If you make use of VCFtools in your research, the authors would
|
||||
appreciate a citation of the following paper:
|
||||
|
||||
The Variant Call Format and VCFtools,
|
||||
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers,
|
||||
Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter,
|
||||
Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin
|
||||
and 1000 Genomes Project Analysis Group, Bioinformatics, 2011
|
||||
|
||||
http://dx.doi.org/10.1093/bioinformatics/btr330
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
Description: do not use MAKEFLAGS
|
||||
Author: Thorsten Alteholz <debian@alteholz.de>
|
||||
Last-Update: 2011-07-03
|
||||
Index: vcftools-0.1.7/Makefile
|
||||
===================================================================
|
||||
--- vcftools_0.1.7.org/Makefile 2011-07-04 15:22:33.000000000 +0200
|
||||
+++ vcftools_0.1.7/Makefile 2011-07-04 15:22:56.000000000 +0200
|
||||
@@ -22,7 +22,7 @@
|
||||
DIRS = cpp perl
|
||||
install:
|
||||
@mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
|
||||
- for dir in $(DIRS); do cd $$dir && $(MAKE) $(MAKEFLAGS) && cd ..; done
|
||||
+ for dir in $(DIRS); do cd $$dir && $(MAKE) && cd ..; done
|
||||
|
||||
clean:
|
||||
@for dir in $(DIRS); do cd $$dir && $(MAKE) clean && cd ..; done
|
||||
|
|
@ -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------------------------------------------------------|
|
||||
vcftools: vcftools (A program package designed for working with VCF files)
|
||||
vcftools:
|
||||
vcftools: VCFtools is a program package designed for working with VCF
|
||||
vcftools: files such as those generated by the 1000 Genomes Project.
|
||||
vcftools: The aim of VCFtools is to provide methods for working with
|
||||
vcftools: VCF files: validating, merging, comparing and calculate some
|
||||
vcftools: basic population genetic statistics.
|
||||
vcftools:
|
||||
vcftools: Home: http://vcftools.sourceforge.net/
|
||||
vcftools: References: /usr/doc/vcftools-0.1.11/References
|
||||
vcftools:
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
Author: Andreas Tille <tille@debian.org>
|
||||
Date: Sat, 12 May 2012 09:31:58 +0200
|
||||
Description: Enable propagation of hardening flags
|
||||
|
||||
Index: vcftools_0.1.11/cpp/Makefile
|
||||
===================================================================
|
||||
--- vcftools_0.1.11.orig/cpp/Makefile 2013-06-13 16:40:54.000000000 +0200
|
||||
+++ vcftools_0.1.11/cpp/Makefile 2013-06-27 19:54:45.000000000 +0200
|
||||
@@ -12,9 +12,9 @@
|
||||
VCFTOOLS_PCA = 0
|
||||
endif
|
||||
# Compiler flags
|
||||
-CFLAGS = -O2 -m64
|
||||
+CFLAGS += -O2
|
||||
#CFLAGS = -Wall -O2 -pg -m64
|
||||
-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64
|
||||
+CPPFLAGS += -O2 -D_FILE_OFFSET_BITS=64
|
||||
#CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
|
||||
# Included libraries (zlib)
|
||||
LIB = -lz
|
||||
@@ -38,7 +38,7 @@
|
||||
endif
|
||||
|
||||
vcftools: $(OBJS)
|
||||
- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
|
||||
+ $(CPP) $(CPPFLAGS) $(OBJS) $(LDFLAGS) -o vcftools $(LIB)
|
||||
ifdef BINDIR
|
||||
cp $(CURDIR)/$@ $(BINDIR)/$@
|
||||
endif
|
||||
@@ -50,8 +50,8 @@
|
||||
-include $(OBJS:.o=.d)
|
||||
|
||||
%.o: %.cpp
|
||||
- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
|
||||
- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
|
||||
+ $(CPP) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp -o $*.o
|
||||
+ $(CPP) -MM $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp > $*.d
|
||||
|
||||
# remove compilation products
|
||||
clean:
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
#!/bin/sh
|
||||
|
||||
# Slackware build script for vcftools
|
||||
|
||||
# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
|
||||
# All rights reserved.
|
||||
#
|
||||
# Redistribution and use of this script, with or without modification, is
|
||||
# permitted provided that the following conditions are met:
|
||||
#
|
||||
# 1. Redistributions of this script must retain the above copyright
|
||||
# notice, this list of conditions and the following disclaimer.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
|
||||
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
|
||||
# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
||||
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
|
||||
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
|
||||
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
|
||||
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
PRGNAM=vcftools
|
||||
VERSION=${VERSION:-0.1.11}
|
||||
BUILD=${BUILD:-1}
|
||||
TAG=${TAG:-_SBo}
|
||||
|
||||
if [ -z "$ARCH" ]; then
|
||||
case "$( uname -m )" in
|
||||
i?86) ARCH=i486 ;;
|
||||
arm*) ARCH=arm ;;
|
||||
*) ARCH=$( uname -m ) ;;
|
||||
esac
|
||||
fi
|
||||
|
||||
CWD=$(pwd)
|
||||
TMP=${TMP:-/tmp/SBo}
|
||||
PKG=$TMP/package-$PRGNAM
|
||||
OUTPUT=${OUTPUT:-/tmp}
|
||||
|
||||
if [ "$ARCH" = "i486" ]; then
|
||||
SLKCFLAGS="-O2 -march=i486 -mtune=i686"
|
||||
LIBDIRSUFFIX=""
|
||||
elif [ "$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.gz
|
||||
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 {} \;
|
||||
|
||||
# Thanks to Debian for the patches
|
||||
patch -p1 -i $CWD/make.patch
|
||||
patch -p1 -i $CWD/use-dpkg-buildflags.patch
|
||||
|
||||
# Set the proper, architecture-specific path
|
||||
sed -i "s:/lib/perl5/site_perl:/lib${LIBDIRSUFFIX}/perl5:g" Makefile
|
||||
|
||||
# It seems that if you run just "make" as root, it will _install_ the
|
||||
# executables and perl files before the package is even created...
|
||||
CFLAGS="$SLKCFLAGS" \
|
||||
CPPFLAGS="$SLKCFLAGS" \
|
||||
PREFIX=$PKG/usr \
|
||||
make install
|
||||
|
||||
# Copy examples
|
||||
mkdir -p $PKG/usr/share/$PRGNAM
|
||||
cp -a examples $PKG/usr/share/$PRGNAM
|
||||
|
||||
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 \
|
||||
README.txt perl/ChangeLog website/*.pdf \
|
||||
$PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
|
||||
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
|
||||
|
||||
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}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
PRGNAM="vcftools"
|
||||
VERSION="0.1.11"
|
||||
HOMEPAGE="http://vcftools.sourceforge.net/"
|
||||
DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.11.tar.gz"
|
||||
MD5SUM="ddb49e9fa2bfedae36b4dce163adfaa8"
|
||||
DOWNLOAD_x86_64=""
|
||||
MD5SUM_x86_64=""
|
||||
REQUIRES=""
|
||||
MAINTAINER="Petar Petrov"
|
||||
EMAIL="petar.petrov@student.oulu.fi"
|
||||
Loading…
Reference in New Issue