From 488f7c2161fe9b6d89651352992ba8ab7121759f Mon Sep 17 00:00:00 2001
From: Petar Petrov <petar.petrov@student.oulu.fi>
Date: Wed, 9 Apr 2014 17:19:20 +0700
Subject: [PATCH] academic/vcftools: Updated for version 0.1.12a.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/vcftools/make.patch          | 17 ++++++++++-------
 academic/vcftools/slack-desc          |  2 +-
 academic/vcftools/vcftools.SlackBuild | 11 ++++++-----
 academic/vcftools/vcftools.info       |  6 +++---
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/academic/vcftools/make.patch b/academic/vcftools/make.patch
index f7cc48b93d..7c3ff55deb 100644
--- a/academic/vcftools/make.patch
+++ b/academic/vcftools/make.patch
@@ -1,15 +1,18 @@
-Description: do not use MAKEFLAGS
+Description: do not use MAKEFLAGS and not MANDIR
 Author: Thorsten Alteholz <debian@alteholz.de>
-Last-Update: 2011-07-03
-Index: vcftools-0.1.7/Makefile
+Last-Update: 2014-04-03
+Index: vcftools_0.1.12/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 @@
+--- 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 $(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:
diff --git a/academic/vcftools/slack-desc b/academic/vcftools/slack-desc
index a15655731f..6589ecf88c 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-0.1.11/References
+vcftools: References: /usr/doc/vcftools-0.1.12a/References
 vcftools:
diff --git a/academic/vcftools/vcftools.SlackBuild b/academic/vcftools/vcftools.SlackBuild
index 506bba88d1..4c69a76a95 100644
--- a/academic/vcftools/vcftools.SlackBuild
+++ b/academic/vcftools/vcftools.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for vcftools
 
-# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
+# Copyright 2013-2014 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=${VERSION:-0.1.11}
+VERSION=${VERSION:-0.1.12a}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -83,6 +83,9 @@ CPPFLAGS="$SLKCFLAGS" \
 PREFIX=$PKG/usr \
 make install
 
+# Copy man page
+install -D -m644 cpp/vcftools.1.gz $PKG/usr/man/man1/vcftools.1.gz
+
 # Copy examples
 mkdir -p $PKG/usr/share/$PRGNAM
 cp -a examples $PKG/usr/share/$PRGNAM
@@ -91,9 +94,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
   | 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
+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
 
diff --git a/academic/vcftools/vcftools.info b/academic/vcftools/vcftools.info
index b754295189..77a7dab1c5 100644
--- a/academic/vcftools/vcftools.info
+++ b/academic/vcftools/vcftools.info
@@ -1,8 +1,8 @@
 PRGNAM="vcftools"
-VERSION="0.1.11"
+VERSION="0.1.12a"
 HOMEPAGE="http://vcftools.sourceforge.net/"
-DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.11.tar.gz"
-MD5SUM="ddb49e9fa2bfedae36b4dce163adfaa8"
+DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12a.tar.gz"
+MD5SUM="ca2ab768ed741623263dbe123cac428b"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""