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academic/bowtie2: Updated for version 2.3.4.3 + new maintainer.

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Rob van Nues 2018-12-30 08:02:32 +07:00 committed by Willy Sudiarto Raharjo
parent 8ec5aafc57
commit 5a353968a9
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GPG key ID: 887B8374D7333381
4 changed files with 27 additions and 25 deletions
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3
academic/bowtie2/References
View file

@ -1,3 +0,0 @@
Please cite:
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2.
Nature Methods. 2012, 9:357-359.

29
academic/bowtie2/bowtie2.SlackBuild
View file

@ -3,6 +3,8 @@
# Slackware build script for bowtie2
# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
# Copyright 2018 Rob van Nues sborg63@disroot.org
#
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -22,14 +24,14 @@
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=bowtie2
VERSION=${VERSION:-2.1.0}
PRGNAM=bowtie2
VERSION=${VERSION:-2.3.4.3}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i486 ;;
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
@ -40,8 +42,8 @@ TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i486" ]; then
SLKCFLAGS="-O2 -march=i486 -mtune=i686"
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "i686" ]; then
SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@ -60,7 +62,7 @@ rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION
unzip $CWD/$PRGNAM-$VERSION-source.zip
tar -xvzf $CWD/$PRGNAM-$VERSION.tar.gz
cd $PRGNAM-$VERSION
chown -R root:root .
find -L . \
@ -69,16 +71,20 @@ 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 {} \;
#Use our FLAGS
sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile
#sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile
RELEASE_FLAGS="$SLKCFLAGS" \
RELEASE_FLAGS+="$SLKCFLAGS" \
make
install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
install -D -m755 $PRGNAM-align $PKG/usr/bin/$PRGNAM-align
install -D -m755 $PRGNAM-align-l $PKG/usr/bin/$PRGNAM-align-l
install -D -m755 $PRGNAM-build-l $PKG/usr/bin/$PRGNAM-build-l
install -D -m755 $PRGNAM-align-s $PKG/usr/bin/$PRGNAM-align-s
install -D -m755 $PRGNAM-build-s $PKG/usr/bin/$PRGNAM-build-s
install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build
install -D -m755 $PRGNAM-inspect-l $PKG/usr/bin/$PRGNAM-inspect-l
install -D -m755 $PRGNAM-inspect-s $PKG/usr/bin/$PRGNAM-inspect-s
install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect
# Copy examples and scripts
@ -86,7 +92,7 @@ mkdir -p $PKG/usr/share/$PRGNAM
cp -a \
example scripts \
$PKG/usr/share/$PRGNAM
# Let's compress the reads and indexes
gzip $PKG/usr/share/$PRGNAM/example/reads/*.fq
gzip $PKG/usr/share/$PRGNAM/example/index/*.bt2
@ -99,7 +105,6 @@ cp -a \
AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \
$PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
mkdir -p $PKG/install
cat $CWD/slack-desc > $PKG/install/slack-desc

14
academic/bowtie2/bowtie2.info
View file

@ -1,10 +1,10 @@
PRGNAM="bowtie2"
VERSION="2.1.0"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
DOWNLOAD="http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/bowtie2-2.1.0-source.zip"
MD5SUM="1d10f079d6dd560320f0309bd70f6080"
VERSION="2.3.4.3"
HOMEPAGE="https://github.com/BenLangmead/bowtie2/releases"
DOWNLOAD="https://github.com/BenLangmead/bowtie2/archive/v2.3.4.3/bowtie2-2.3.4.3.tar.gz"
MD5SUM="9f8bb660362813277d12580da551b0c7"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"
REQUIRES="tbb"
MAINTAINER="Rob van Nues"
EMAIL="sborg63@disroot.org"

6
academic/bowtie2/slack-desc
View file

@ -14,6 +14,6 @@ bowtie2: good at aligning reads of about 50 up to 100s or 1,000s of
bowtie2: characters, and particularly good at aligning to relatively long
bowtie2: (e.g. mammalian) genomes.
bowtie2:
bowtie2: Home: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
bowtie2: References: /usr/doc/bowtie2-2.1.0/References
bowtie2:
bowtie2: Home: https://bowtie-bio.sf.net/bowtie2
bowtie2: Reference: Langmead B, Salzberg S. Fast gapped-read alignment with
bowtie2: Bowtie 2. Nature Methods. 2012, 9:357-359.