diff options
Diffstat (limited to 'academic')
-rw-r--r-- | academic/bedtools/README | 11 | ||||
-rw-r--r-- | academic/bedtools/bedtools.SlackBuild | 101 | ||||
-rw-r--r-- | academic/bedtools/bedtools.info | 10 | ||||
-rw-r--r-- | academic/bedtools/slack-desc | 19 |
4 files changed, 141 insertions, 0 deletions
diff --git a/academic/bedtools/README b/academic/bedtools/README new file mode 100644 index 0000000000..d9e5aa3fd4 --- /dev/null +++ b/academic/bedtools/README @@ -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. diff --git a/academic/bedtools/bedtools.SlackBuild b/academic/bedtools/bedtools.SlackBuild new file mode 100644 index 0000000000..968e58da99 --- /dev/null +++ b/academic/bedtools/bedtools.SlackBuild @@ -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} diff --git a/academic/bedtools/bedtools.info b/academic/bedtools/bedtools.info new file mode 100644 index 0000000000..d1080797df --- /dev/null +++ b/academic/bedtools/bedtools.info @@ -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" diff --git a/academic/bedtools/slack-desc b/academic/bedtools/slack-desc new file mode 100644 index 0000000000..7abe9d2c75 --- /dev/null +++ b/academic/bedtools/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------------------------------------------------------| +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: |