diff options
| -rw-r--r-- | academic/bowtie2-legacy/README | 18 | ||||
| -rw-r--r-- | academic/bowtie2-legacy/References | 3 | ||||
| -rw-r--r-- | academic/bowtie2-legacy/bowtie2-legacy.SlackBuild | 110 | ||||
| -rw-r--r-- | academic/bowtie2-legacy/bowtie2-legacy.info | 10 | ||||
| -rw-r--r-- | academic/bowtie2-legacy/slack-desc | 19 |
5 files changed, 160 insertions, 0 deletions
diff --git a/academic/bowtie2-legacy/README b/academic/bowtie2-legacy/README new file mode 100644 index 0000000000..6cdaa72662 --- /dev/null +++ b/academic/bowtie2-legacy/README @@ -0,0 +1,18 @@ +Bowtie 2 is an ultrafast and memory-efficient tool for aligning +sequencing reads to long reference sequences. It is particularly good +at aligning reads of about 50 up to 100s or 1,000s of characters, and +particularly good at aligning to relatively long (e.g. mammalian) +genomes. Bowtie 2 indexes the genome with an FM Index to keep its +memory footprint small: for the human genome, its memory footprint is +typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired- +end alignment modes. + +NOTE! +This is an older version of the program, kept here for compatibility +with Ugene. You can safely install it along the new one. When you start +Ugene, go to Settings > Preferences > External Tools and manually select +the legacy binaries in /usr/bin/ + +Please cite: +Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. +Nature Methods. 2012, 9:357-359. diff --git a/academic/bowtie2-legacy/References b/academic/bowtie2-legacy/References new file mode 100644 index 0000000000..6e3a6e99d0 --- /dev/null +++ b/academic/bowtie2-legacy/References @@ -0,0 +1,3 @@ +Please cite: +Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. +Nature Methods. 2012, 9:357-359. diff --git a/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild new file mode 100644 index 0000000000..db90b9ad1c --- /dev/null +++ b/academic/bowtie2-legacy/bowtie2-legacy.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/sh + +# Slackware build script for bowtie2-legacy + +# Copyright 2013-2018 Petar Petrov slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +SRCNAM=bowtie2 +SUFFIX=legacy +PRGNAM=$SRCNAM-$SUFFIX +VERSION=${VERSION:-2.1.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +unzip $CWD/$SRCNAM-$VERSION-source.zip +cd $SRCNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# Use our FLAGS +sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile + +RELEASE_FLAGS="$SLKCFLAGS" \ +make + +install -D -m755 $SRCNAM $PKG/usr/bin/$PRGNAM +install -D -m755 $SRCNAM-align $PKG/usr/bin/$PRGNAM-align +install -D -m755 $SRCNAM-build $PKG/usr/bin/$PRGNAM-build +install -D -m755 $SRCNAM-inspect $PKG/usr/bin/$PRGNAM-inspect + +# Copy examples and scripts +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 + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +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 + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/bowtie2-legacy/bowtie2-legacy.info b/academic/bowtie2-legacy/bowtie2-legacy.info new file mode 100644 index 0000000000..6e8d5c4f1a --- /dev/null +++ b/academic/bowtie2-legacy/bowtie2-legacy.info @@ -0,0 +1,10 @@ +PRGNAM="bowtie2-legacy" +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" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bowtie2-legacy/slack-desc b/academic/bowtie2-legacy/slack-desc new file mode 100644 index 0000000000..4270e5bcd8 --- /dev/null +++ b/academic/bowtie2-legacy/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +bowtie2-legacy: bowtie2-legacy (A tool for aligning sequencing reads) +bowtie2-legacy: +bowtie2-legacy: Bowtie 2 is an ultrafast and memory-efficient tool for aligning +bowtie2-legacy: sequencing reads to long reference sequences. It is particularly +bowtie2-legacy: good at aligning reads of about 50 up to 100s or 1,000s of +bowtie2-legacy: characters, and particularly good at aligning to relatively long +bowtie2-legacy: (e.g. mammalian) genomes. +bowtie2-legacy: +bowtie2-legacy: Home: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml +bowtie2-legacy: References: /usr/doc/bowtie2-2.1.0/References +bowtie2-legacy: |