academic/bedtools: Added (genome arithmetic).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 141 insertions, 0 deletions

diff --git a/academic/bedtools/README b/academic/bedtools/README
new file mode 100644
index 0000000000000..d9e5aa3fd405a
--- /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 0000000000000..968e58da9925d
--- /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 0000000000000..d1080797df1f1
--- /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 0000000000000..7abe9d2c75412
--- /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: