academic/bowtie2-legacy: Added (aligning sequencing reads).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
f240a7ca47
commit
1fecb5b64f
|
|
@ -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.
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
Please cite:
|
||||
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2.
|
||||
Nature Methods. 2012, 9:357-359.
|
||||
|
|
@ -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}
|
||||
|
|
@ -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"
|
||||
|
|
@ -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:
|
||||
Loading…
Reference in New Issue