academic/bedGraphToBigWig: Added (Convert bedGraph to bigWig file)

4 files changed, 102 insertions, 0 deletions

diff --git a/academic/bedGraphToBigWig/README b/academic/bedGraphToBigWig/README
new file mode 100644
index 0000000000000..81fd8910edc68
--- /dev/null
+++ b/academic/bedGraphToBigWig/README
@@ -0,0 +1,7 @@
+Convert bedGraph to bigWig file. Description of Big Binary Indexed
+(BBI) files and visualization of next-generation sequencing experiment
+results explained by W.J. Kent, PMCID: PMC2922891
+
+This just repackages the binary distributed by the Ugene Project, part
+of their External Tools package. It is hosted on Source Forge by the
+SlackBuild maintainer.
diff --git a/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild
new file mode 100644
index 0000000000000..b270b511bc3e1
--- /dev/null
+++ b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild
@@ -0,0 +1,66 @@
+#!/bin/sh
+
+# Slackware build script for bedGraphToBigWig
+
+# Copyright 2016 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.
+
+PRGNAM=bedGraphToBigWig
+VERSION=${VERSION:-4}
+BUILD=${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=${OUTPUT:-/tmp}
+
+set -e
+
+if [ "$ARCH" != "x86_64" ]; then
+  printf "\n\n$ARCH is not supported... \n"
+  exit 1
+fi
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $PRGNAM-$VERSION
+
+install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
+
+mkdir -p $PKG/usr/doc/$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/bedGraphToBigWig/bedGraphToBigWig.info b/academic/bedGraphToBigWig/bedGraphToBigWig.info
new file mode 100644
index 0000000000000..8d10db77520b0
--- /dev/null
+++ b/academic/bedGraphToBigWig/bedGraphToBigWig.info
@@ -0,0 +1,10 @@
+PRGNAM="bedGraphToBigWig"
+VERSION="4"
+HOMEPAGE="https://www.encodeproject.org/software/bedgraphtobigwig/"
+DOWNLOAD="UNSUPPORTED"
+MD5SUM=""
+DOWNLOAD_x86_64="http://sourceforge.net/projects/sboppetrov/files/bedGraphToBigWig/bedGraphToBigWig-4.tar.gz"
+MD5SUM_x86_64="5b012409c804b79607b675b52369d487"
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/bedGraphToBigWig/slack-desc b/academic/bedGraphToBigWig/slack-desc
new file mode 100644
index 0000000000000..eeb54bf94c7e6
--- /dev/null
+++ b/academic/bedGraphToBigWig/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------------------------------------------------------|
+bedGraphToBigWig: bedGraphToBigWig (Convert bedGraph to bigWig file)
+bedGraphToBigWig:
+bedGraphToBigWig: Convert bedGraph to bigWig file. For more information
+bedGraphToBigWig: see the links below.
+bedGraphToBigWig: https://www.encodeproject.org/software/bedgraphtobigwig/
+bedGraphToBigWig: http://ugene.net/external.html
+bedGraphToBigWig: http://hgdownload.cse.ucsc.edu/admin/exe/
+bedGraphToBigWig:
+bedGraphToBigWig:
+bedGraphToBigWig:
+bedGraphToBigWig: