diff options
Diffstat (limited to 'academic/fastqc/fastqc.SlackBuild')
| -rw-r--r-- | academic/fastqc/fastqc.SlackBuild | 31 |
1 files changed, 22 insertions, 9 deletions
diff --git a/academic/fastqc/fastqc.SlackBuild b/academic/fastqc/fastqc.SlackBuild index 72021c6af6..c8127dac3f 100644 --- a/academic/fastqc/fastqc.SlackBuild +++ b/academic/fastqc/fastqc.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for fastqc -# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018 Rob van Nues sborg63.org +# Copyright 2015-2018 Petar Petrov slackalaxy@gmail.com; 2018-2023 Rob van Nues sborg63.org # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,22 +22,32 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +cd $(dirname $0) ; CWD=$(pwd) + PRGNAM=fastqc SRCNAM=FastQC -VERSION=${VERSION:-0.11.8} -SRCVER=${SRCVER:-v0.11.8} +VERSION=${VERSION:-0.12.1} +SRCVER=${SRCVER:-v0.12.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} ARCH=noarch # Jar files names and versions JBZIP=jbzip2-0.9.jar -SAM=sam-1.103.jar +HTS=htsjdk.jar CISD=cisd-jhdf5.jar -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -57,8 +67,11 @@ 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 {} \; +# remove .svn folders causing java errors e.g. when using help +find -d -name .svn -exec rm -r '{}' ';' + install -D -m755 $PRGNAM $PKG/usr/share/java/$PRGNAM/$PRGNAM -cp -a Configuration net org Templates Help uk $JBZIP $SAM $CISD $PKG/usr/share/java/$PRGNAM +cp -a Configuration net org Templates Help uk $JBZIP $HTS $CISD $PKG/usr/share/java/$PRGNAM mkdir -p $PKG/usr/bin cd $PKG/usr/bin @@ -85,4 +98,4 @@ cat $CWD/slack-desc > $PKG/install/slack-desc cat $CWD/doinst.sh > $PKG/install/doinst.sh cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE |