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

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 27 insertions, 25 deletions

diff --git a/academic/bowtie2/References b/academic/bowtie2/References
deleted file mode 100644
index 6e3a6e99d0..0000000000
--- a/academic/bowtie2/References
+++ /dev/null
@@ -1,3 +0,0 @@
-Please cite:
-Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2.
-Nature Methods. 2012, 9:357-359.
diff --git a/academic/bowtie2/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild
index 43c3392d90..f113b58359 100644
--- a/academic/bowtie2/bowtie2.SlackBuild
+++ b/academic/bowtie2/bowtie2.SlackBuild
@@ -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
diff --git a/academic/bowtie2/bowtie2.info b/academic/bowtie2/bowtie2.info
index aca3d2fbd6..bb5332d8c3 100644
--- a/academic/bowtie2/bowtie2.info
+++ b/academic/bowtie2/bowtie2.info
@@ -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"
diff --git a/academic/bowtie2/slack-desc b/academic/bowtie2/slack-desc
index b65813fb52..fbdddad984 100644
--- a/academic/bowtie2/slack-desc
+++ b/academic/bowtie2/slack-desc
@@ -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.