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academic/PhyML: Updated for version 20130219.

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Signed-off-by: dsomero <xgizzmo@slackbuilds.org>
This commit is contained in:
Petar Petrov 2013-03-11 19:29:34 -04:00 committed by dsomero
parent f3ff891906
commit 5ff74fd3f1
4 changed files with 1536 additions and 11 deletions
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1519
academic/PhyML/20130219.patch Normal file
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16
academic/PhyML/PhyML.SlackBuild
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@ -2,7 +2,7 @@
# Slackware build script for PhyML
# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi
# Copyright 2011-2013 Petar Petrov, ppetrov@paju.oulu.fi
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -25,11 +25,12 @@
# Thanks to Niels Horn for some handy modifications and corrections.
PRGNAM=PhyML
VERSION=${VERSION:-20120412}
VERSION=${VERSION:-20130219}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
SRCVER=20120412
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
@ -63,9 +64,9 @@ set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $SRCNAM-$VERSION
tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
cd $SRCNAM-$VERSION
rm -rf $SRCNAM-$SRCVER
tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
cd $SRCNAM-$SRCVER
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
@ -73,6 +74,11 @@ find . \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
# Apply patch 20130219
cd src
patch -i $CWD/$VERSION.patch
cd ..
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \

2
academic/PhyML/PhyML.info
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@ -1,5 +1,5 @@
PRGNAM="PhyML"
VERSION="20120412"
VERSION="20130219"
HOMEPAGE="http://code.google.com/p/phyml/"
DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz"
MD5SUM="d2207a3d6caf633c43239a01ce70f244"

10
academic/PhyML/slack-desc
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@ -1,9 +1,9 @@
# 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 ':'.
# 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------------------------------------------------------|
PhyML: PhyML (Phylogenetic estimation using Maximum Likelihood)