mirror of
https://github.com/Ponce/slackbuilds
synced 2024-10-01 06:32:51 +02:00
academic/bedtools: Added (genome arithmetic).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
parent
aa58ad6fb2
commit
feb7ad033a
4 changed files with 141 additions and 0 deletions
11
academic/bedtools/README
Normal file
11
academic/bedtools/README
Normal file
|
@ -0,0 +1,11 @@
|
|||
Collectively, the bedtools utilities are a swiss-army knife of tools
|
||||
for a wide-range of genomics analysis tasks. The most widely-used
|
||||
tools enable genome arithmetic: that is, set theory on the genome. For
|
||||
example, bedtools allows one to intersect, merge, count, complement,
|
||||
and shuffle genomic intervals from multiple files in widely-used
|
||||
genomic file formats such as BAM, BED, GFF/GTF, VCF.
|
||||
|
||||
While each individual tool is designed to do a relatively simple task
|
||||
(e.g., intersect two interval files), quite sophisticated analyses can
|
||||
be conducted by combining multiple bedtools operations on the UNIX
|
||||
command line.
|
101
academic/bedtools/bedtools.SlackBuild
Normal file
101
academic/bedtools/bedtools.SlackBuild
Normal file
|
@ -0,0 +1,101 @@
|
|||
#!/bin/sh
|
||||
|
||||
# Slackware build script for bedtools
|
||||
|
||||
# Copyright 2014 Petar Petrov, petar.petrov@student.oulu.fi
|
||||
# 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.
|
||||
|
||||
PRGNAM=bedtools
|
||||
DIRNAM=bedtools2
|
||||
VERSION=${VERSION:-2.21.0}
|
||||
BUILD=${BUILD:-1}
|
||||
TAG=${TAG:-_SBo}
|
||||
|
||||
if [ -z "$ARCH" ]; then
|
||||
case "$( uname -m )" in
|
||||
i?86) ARCH=i486 ;;
|
||||
arm*) ARCH=arm ;;
|
||||
*) ARCH=$( uname -m ) ;;
|
||||
esac
|
||||
fi
|
||||
|
||||
CWD=$(pwd)
|
||||
TMP=${TMP:-/tmp/SBo}
|
||||
PKG=$TMP/package-$PRGNAM
|
||||
OUTPUT=${OUTPUT:-/tmp}
|
||||
|
||||
if [ "$ARCH" = "i486" ]; then
|
||||
SLKCFLAGS="-O2 -march=i486 -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 $DIRNAM
|
||||
tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
|
||||
cd $DIRNAM
|
||||
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 CFLAGS
|
||||
sed -i "/CXXFLAGS/s/=/+=/" Makefile
|
||||
|
||||
CXXFLAGS="$SLKCFLAGS" \
|
||||
make
|
||||
|
||||
# Install the binary and scripts
|
||||
cd bin
|
||||
for i in * ; do
|
||||
install -D -m755 $i $PKG/usr/bin/$i
|
||||
done
|
||||
cd ..
|
||||
|
||||
# Copy additional data
|
||||
mkdir -p $PKG/usr/share/$PRGNAM
|
||||
cp -a data genomes scripts $PKG/usr/share/$PRGNAM
|
||||
|
||||
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 LICENSE README.md RELEASE_HISTORY $PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
|
||||
|
||||
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}
|
10
academic/bedtools/bedtools.info
Normal file
10
academic/bedtools/bedtools.info
Normal file
|
@ -0,0 +1,10 @@
|
|||
PRGNAM="bedtools"
|
||||
VERSION="2.21.0"
|
||||
HOMEPAGE="http://bedtools.readthedocs.org/"
|
||||
DOWNLOAD="https://github.com/arq5x/bedtools2/releases/download/v2.21.0/bedtools-2.21.0.tar.gz"
|
||||
MD5SUM="42cf57a5f110e06aa666aed58e0c3064"
|
||||
DOWNLOAD_x86_64=""
|
||||
MD5SUM_x86_64=""
|
||||
REQUIRES=""
|
||||
MAINTAINER="Petar Petrov"
|
||||
EMAIL="petar.petrov@student.oulu.fi"
|
19
academic/bedtools/slack-desc
Normal file
19
academic/bedtools/slack-desc
Normal file
|
@ -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------------------------------------------------------|
|
||||
bedtools: bedtools (A powerful toolset for genome arithmetic)
|
||||
bedtools:
|
||||
bedtools: The bedtools utilities are a swiss-army knife of tools for a
|
||||
bedtools: wide-range of genomics analysis tasks. The most widely-used
|
||||
bedtools: tools enable genome arithmetic: that is, set theory on the
|
||||
bedtools: genome.
|
||||
bedtools:
|
||||
bedtools: Home: http://bedtools.readthedocs.org/
|
||||
bedtools:
|
||||
bedtools:
|
||||
bedtools:
|
Loading…
Reference in a new issue