academic/vcftools: Updated for version 0.1.14_2_g78add55.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
c61d2947f7
commit
72a5c0c201
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@ -15,5 +15,5 @@ vcftools: VCF files: validating, merging, comparing and calculate some
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vcftools: basic population genetic statistics.
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vcftools:
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vcftools: Home: http://vcftools.sourceforge.net/
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vcftools: References: /usr/doc/vcftools-0.1.12b/References
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vcftools: References: /usr/doc/vcftools-0.1.14_2_g78add55/References
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vcftools:
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@ -1,40 +0,0 @@
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Author: Andreas Tille <tille@debian.org>
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Date: Sat, 12 May 2012 09:31:58 +0200
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Description: Enable propagation of hardening flags
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Index: vcftools_0.1.11/cpp/Makefile
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===================================================================
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--- vcftools_0.1.11.orig/cpp/Makefile 2013-06-13 16:40:54.000000000 +0200
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+++ vcftools_0.1.11/cpp/Makefile 2013-06-27 19:54:45.000000000 +0200
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@@ -12,9 +12,9 @@
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VCFTOOLS_PCA = 0
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endif
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# Compiler flags
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-CFLAGS = -O2 -m64
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+CFLAGS += -O2
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#CFLAGS = -Wall -O2 -pg -m64
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-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64
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+CPPFLAGS += -O2 -D_FILE_OFFSET_BITS=64
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#CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
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# Included libraries (zlib)
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LIB = -lz
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@@ -38,7 +38,7 @@
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endif
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vcftools: $(OBJS)
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- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
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+ $(CPP) $(CPPFLAGS) $(OBJS) $(LDFLAGS) -o vcftools $(LIB)
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ifdef BINDIR
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cp $(CURDIR)/$@ $(BINDIR)/$@
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endif
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@@ -50,8 +50,8 @@
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-include $(OBJS:.o=.d)
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%.o: %.cpp
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- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
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- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
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+ $(CPP) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp -o $*.o
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+ $(CPP) -MM $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp > $*.d
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# remove compilation products
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clean:
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@ -23,10 +23,13 @@
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=vcftools
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VERSION=${VERSION:-0.1.12b}
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VERSION=${VERSION:-0.1.14_2_g78add55}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCVER=v0.1.14-2-g78add55
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GITVER=78add55
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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@ -59,9 +62,9 @@ set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf ${PRGNAM}_${VERSION}
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tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz
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cd ${PRGNAM}_${VERSION}
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rm -rf ${PRGNAM}-${PRGNAM}-${SRCVER}
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tar xvf $CWD/${PRGNAM}-${PRGNAM}-${SRCVER}.tar.gz
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cd ${PRGNAM}-${PRGNAM}-${GITVER}
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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@ -69,21 +72,19 @@ find -L . \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Thanks to Debian for the patch
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patch -p1 -i $CWD/use-dpkg-buildflags.patch
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# Set the proper, architecture-specific path
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sed -i "s:/lib/perl5/site_perl:/lib${LIBDIRSUFFIX}/perl5:g" Makefile
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./autogen.sh
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CFLAGS="$SLKCFLAGS" \
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CPPFLAGS="$SLKCFLAGS" \
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PREFIX=$PKG/usr \
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make install
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# Remove this and copy the man page to its proper place
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rm -rf $PKG/usr/bin/man1
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mkdir -p $PKG//usr/man/man1
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cp cpp/vcftools.1 $PKG/usr/man/man1
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib${LIBDIRSUFFIX} \
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--sysconfdir=/etc \
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--localstatedir=/var \
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--mandir=/usr/man \
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--docdir=/usr/doc/$PRGNAM-$VERSION \
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--build=$ARCH-slackware-linux
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make
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make DESTDIR=$PKG install
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# Copy examples
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mkdir -p $PKG/usr/share/$PRGNAM
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@ -96,7 +97,7 @@ find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a README.txt perl/ChangeLog website/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a README.md src/perl/ChangeLog $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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@ -1,8 +1,8 @@
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PRGNAM="vcftools"
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VERSION="0.1.12b"
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HOMEPAGE="http://vcftools.sourceforge.net/"
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DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12b.tar.gz"
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MD5SUM="662758d1139c138cf5a0239ed99f12c2"
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VERSION="0.1.14_2_g78add55"
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HOMEPAGE="https://vcftools.github.io/"
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DOWNLOAD="https://github.com/vcftools/vcftools/tarball/master/vcftools-vcftools-v0.1.14-2-g78add55.tar.gz"
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MD5SUM="e5fbb773ef13d567606067351501ac13"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="tabix"
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