academic/vcftools: Added (A program designed for working with VCF).

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

7 files changed, 217 insertions, 0 deletions

diff --git a/academic/vcftools/README b/academic/vcftools/README
new file mode 100644
index 0000000000..de03f3235e
--- /dev/null
+++ b/academic/vcftools/README
@@ -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
diff --git a/academic/vcftools/References b/academic/vcftools/References
new file mode 100644
index 0000000000..03bd303faa
--- /dev/null
+++ b/academic/vcftools/References
@@ -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
diff --git a/academic/vcftools/make.patch b/academic/vcftools/make.patch
new file mode 100644
index 0000000000..f7cc48b93d
--- /dev/null
+++ b/academic/vcftools/make.patch
@@ -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
diff --git a/academic/vcftools/slack-desc b/academic/vcftools/slack-desc
new file mode 100644
index 0000000000..a15655731f
--- /dev/null
+++ b/academic/vcftools/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------------------------------------------------------|
+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:
diff --git a/academic/vcftools/use-dpkg-buildflags.patch b/academic/vcftools/use-dpkg-buildflags.patch
new file mode 100644
index 0000000000..3bd8521a3a
--- /dev/null
+++ b/academic/vcftools/use-dpkg-buildflags.patch
@@ -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 > $*.d
+ 
+ # remove compilation products
+ clean:
diff --git a/academic/vcftools/vcftools.SlackBuild b/academic/vcftools/vcftools.SlackBuild
new file mode 100644
index 0000000000..506bba88d1
--- /dev/null
+++ b/academic/vcftools/vcftools.SlackBuild
@@ -0,0 +1,104 @@
+#!/bin/sh
+
+# Slackware build script for vcftools
+
+# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+PRGNAM=vcftools
+VERSION=${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}
diff --git a/academic/vcftools/vcftools.info b/academic/vcftools/vcftools.info
new file mode 100644
index 0000000000..b754295189
--- /dev/null
+++ b/academic/vcftools/vcftools.info
@@ -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"