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academic/snpEff: Build cleanup.

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Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov 2022-08-12 19:40:44 +01:00 committed by Willy Sudiarto Raharjo
parent 7c900167f3
commit 6bc47f9735
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GPG key ID: 3F617144D7238786
1 changed files with 9 additions and 5 deletions
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14
academic/snpEff/snpEff.SlackBuild
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@ -2,7 +2,7 @@
# Slackware build script for snpEff
# Copyright 2015-2021 Petar Petrov slackalaxy@gmail.com
# Copyright 2015-2022 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -27,7 +27,7 @@ cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=snpEff
VERSION=${VERSION:-4.3t}
SRCVER=${SRCVER:-v4_3t}
BUILD=${BUILD:-1}
BUILD=${BUILD:-2}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
@ -50,7 +50,9 @@ set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM
rm -rf $PRGNAM-$VERSION
mkdir -p $PRGNAM-$VERSION
cd $PRGNAM-$VERSION
unzip $CWD/${PRGNAM}_${SRCVER}_core.zip
cd $PRGNAM
chown -R root:root .
@ -60,8 +62,10 @@ 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 {} \;
mkdir -p $PKG/usr/share/java/$PRGNAM
cp -a examples galaxy scripts $PRGNAM.config $PRGNAM.jar SnpSift.jar \
install -D -m755 $PRGNAM.jar $PKG/usr/share/java/$PRGNAM/$PRGNAM.jar
install -D -m755 SnpSift.jar $PKG/usr/share/java/$PRGNAM/SnpSift.jar
cp -a examples galaxy scripts $PRGNAM.config \
$PKG/usr/share/java/$PRGNAM
mkdir -p $PKG/usr/bin