diff options
| -rw-r--r-- | academic/bowtie2/References | 3 | ||||
| -rw-r--r-- | academic/bowtie2/bowtie2.SlackBuild | 29 | ||||
| -rw-r--r-- | academic/bowtie2/bowtie2.info | 14 | ||||
| -rw-r--r-- | academic/bowtie2/slack-desc | 6 |
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. |