academic/IGV: Added (Integrative Genomics Viewer)

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

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

7 files changed, 148 insertions, 0 deletions

diff --git a/academic/IGV/IGV.SlackBuild b/academic/IGV/IGV.SlackBuild
new file mode 100644
index 0000000000000..746d394ea4da5
--- /dev/null
+++ b/academic/IGV/IGV.SlackBuild
@@ -0,0 +1,84 @@
+#!/bin/sh
+
+# Slackware build script for IGV
+
+# Copyright 2020 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=IGV
+VERSION=${VERSION:-2.8.12}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+JDK=jdk-11
+
+if [ -z "$ARCH" ]; then
+  ARCH="$( uname -m )"
+fi
+
+if [ "$ARCH" != "x86_64" ]; then
+  printf "\n\n$ARCH is not supported... \n" >&2
+  exit 1
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf ${PRGNAM}_Linux_${VERSION}
+unzip $CWD/${PRGNAM}_Linux_${VERSION}_WithJava.zip
+cd ${PRGNAM}_Linux_${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 {} \;
+
+# Place it in /opt and make a symlink later
+mkdir -p $PKG/opt/$PRGNAM
+cp -a $JDK lib igv.args igv.sh igv_hidpi.sh $PKG/opt/$PRGNAM
+
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp IGV_64.png $PKG/usr/share/pixmaps/$PRGNAM.png
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a readme.txt  $PKG/usr/doc/$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/usr/bin
+cd $PKG/usr/bin
+ln -s ../../opt/$PRGNAM/igv.sh igv
+cd -
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/IGV/IGV.desktop b/academic/IGV/IGV.desktop
new file mode 100644
index 0000000000000..9dad30517ebed
--- /dev/null
+++ b/academic/IGV/IGV.desktop
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Type=Application
+Exec=igv
+Terminal=false
+Name=IGV
+Icon=IGV
+Comment=Integrative Genomics Viewer
+Categories=Education;
diff --git a/academic/IGV/IGV.info b/academic/IGV/IGV.info
new file mode 100644
index 0000000000000..f54e6a3a2d975
--- /dev/null
+++ b/academic/IGV/IGV.info
@@ -0,0 +1,10 @@
+PRGNAM="IGV"
+VERSION="2.8.12"
+HOMEPAGE="http://software.broadinstitute.org/software/igv/home"
+DOWNLOAD="UNSUPPORTED"
+MD5SUM=""
+DOWNLOAD_x86_64="https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_Linux_2.8.12_WithJava.zip"
+MD5SUM_x86_64="7ee4f59615726723964bd9e023baf136"
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/IGV/README b/academic/IGV/README
new file mode 100644
index 0000000000000..7c1ec02a11fe1
--- /dev/null
+++ b/academic/IGV/README
@@ -0,0 +1,7 @@
+The Integrative Genomics Viewer (IGV) is a high-performance and easy-to-
+use, interactive tool for the visual exploration of genomic data. It
+supports flexible integration of all the common types of genomic data
+and metadata, investigator-generated or publicly available, loaded from
+local or cloud sources.
+
+Please, check the package's documentation folder for citing information.
diff --git a/academic/IGV/References b/academic/IGV/References
new file mode 100644
index 0000000000000..cdbdf3e743bae
--- /dev/null
+++ b/academic/IGV/References
@@ -0,0 +1,17 @@
+To cite your use of IGV in your publication, please reference one or more of:
+
+James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman,
+Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer.
+Nature Biotechnology 29, 24–26 (2011). (Free PMC article here).
+
+Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov.  
+Integrative Genomics Viewer (IGV): high-performance genomics data visualization
+and exploration. Briefings in Bioinformatics 14, 178-192 (2013).
+
+James T. Robinson, Helga Thorvaldsdóttir, Aaron M. Wenger, Ahmet Zehir, Jill P.
+Mesirov. Variant Review with the Integrative Genomics Viewer (IGV). Cancer
+Research 77(21) 31-34 (2017).
+
+James T. Robinson, Helga Thorvaldsdóttir, Douglass Turner, Jill P. Mesirov.
+igv.js: an embeddable JavaScript implementation of the Integrative Genomics
+Viewer (IGV). bioRxiv 2020.05.03075499.
diff --git a/academic/IGV/doinst.sh b/academic/IGV/doinst.sh
new file mode 100644
index 0000000000000..5fb28930db0b9
--- /dev/null
+++ b/academic/IGV/doinst.sh
@@ -0,0 +1,3 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
diff --git a/academic/IGV/slack-desc b/academic/IGV/slack-desc
new file mode 100644
index 0000000000000..c02edd24c9005
--- /dev/null
+++ b/academic/IGV/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------------------------------------------------------|
+IGV: IGV (Integrative Genomics Viewer)
+IGV:
+IGV: The Integrative Genomics Viewer (IGV) is a high-performance and easy
+IGV: to use, interactive tool for the visual exploration of genomic data.
+IGV: It supports flexible integration of all the common types of genomic
+IGV: data and metadata, investigator-generated or publicly available,
+IGV: loaded from local or cloud sources.
+IGV:
+IGV: http://software.broadinstitute.org/software/igv/home
+IGV:
+IGV: