From ab233795246db630e08c8209fe628490d0c0ff3b Mon Sep 17 00:00:00 2001
From: Petar Petrov <petar.petrov@student.oulu.fi>
Date: Wed, 4 Feb 2015 20:11:28 +0700
Subject: [PATCH] academic/vcftools: Updated for version 0.1.12b.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/vcftools/make.patch          | 19 -------------------
 academic/vcftools/slack-desc          |  2 +-
 academic/vcftools/vcftools.SlackBuild | 18 ++++++++++--------
 academic/vcftools/vcftools.info       |  8 ++++----
 4 files changed, 15 insertions(+), 32 deletions(-)
 delete mode 100644 academic/vcftools/make.patch

diff --git a/academic/vcftools/make.patch b/academic/vcftools/make.patch
deleted file mode 100644
index 7c3ff55deb..0000000000
--- a/academic/vcftools/make.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Description: do not use MAKEFLAGS and not MANDIR
-Author: Thorsten Alteholz <debian@alteholz.de>
-Last-Update: 2014-04-03
-Index: vcftools_0.1.12/Makefile
-===================================================================
---- vcftools_0.1.12.orig/Makefile	2014-04-04 10:37:59.000000000 +0200
-+++ vcftools_0.1.12/Makefile	2014-04-04 10:38:34.000000000 +0200
-@@ -25,9 +25,8 @@
- 
- DIRS = cpp perl
- install:
--	    @mkdir -p $(BINDIR); mkdir -p $(MODDIR); mkdir -p $(MANDIR); \
--	    cp ${PREFIX}/cpp/vcftools.1.gz $(MANDIR); \
--        for dir in $(DIRS); do cd $$dir && $(MAKE) $(MAKEFLAGS) && cd ..; done
-+	    @mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
-+        for dir in $(DIRS); do cd $$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
index 6589ecf88c..7cbadbcbbf 100644
--- a/academic/vcftools/slack-desc
+++ b/academic/vcftools/slack-desc
@@ -15,5 +15,5 @@ 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-0.1.12a/References
+vcftools: References: /usr/doc/vcftools-0.1.12b/References
 vcftools:
diff --git a/academic/vcftools/vcftools.SlackBuild b/academic/vcftools/vcftools.SlackBuild
index 4c69a76a95..624601bdb3 100644
--- a/academic/vcftools/vcftools.SlackBuild
+++ b/academic/vcftools/vcftools.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for vcftools
 
-# Copyright 2013-2014 Petar Petrov, petar.petrov@student.oulu.fi
+# Copyright 2013-2015 Petar Petrov, petar.petrov@student.oulu.fi
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=vcftools
-VERSION=${VERSION:-0.1.12a}
+VERSION=${VERSION:-0.1.12b}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -69,22 +69,21 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Thanks to Debian for the patches
-patch -p1 -i $CWD/make.patch
+# Thanks to Debian for the 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 man page
-install -D -m644 cpp/vcftools.1.gz $PKG/usr/man/man1/vcftools.1.gz
+# Remove this and copy the man page to its proper place
+rm -rf $PKG/usr/bin/man1
+mkdir -p $PKG//usr/man/man1
+cp cpp/vcftools.1 $PKG/usr/man/man1
 
 # Copy examples
 mkdir -p $PKG/usr/share/$PRGNAM
@@ -93,6 +92,9 @@ 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
 
+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 README.txt perl/ChangeLog website/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
diff --git a/academic/vcftools/vcftools.info b/academic/vcftools/vcftools.info
index 77a7dab1c5..e30951603f 100644
--- a/academic/vcftools/vcftools.info
+++ b/academic/vcftools/vcftools.info
@@ -1,10 +1,10 @@
 PRGNAM="vcftools"
-VERSION="0.1.12a"
+VERSION="0.1.12b"
 HOMEPAGE="http://vcftools.sourceforge.net/"
-DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12a.tar.gz"
-MD5SUM="ca2ab768ed741623263dbe123cac428b"
+DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12b.tar.gz"
+MD5SUM="662758d1139c138cf5a0239ed99f12c2"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES=""
+REQUIRES="tabix"
 MAINTAINER="Petar Petrov"
 EMAIL="petar.petrov@student.oulu.fi"