academic/wehi-deid: Added (Flow cytometry De-Identifier).

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

7 files changed, 107 insertions, 0 deletions

diff --git a/academic/wehi-deid/README b/academic/wehi-deid/README
new file mode 100644
index 0000000000..b808b1f009
--- /dev/null
+++ b/academic/wehi-deid/README
@@ -0,0 +1,9 @@
+Flow cytometry De-Identifier
+
+Where flow cytometry data files from the clinic are to be used in
+research projects, DeID is used to remove patient identification. This
+is achieved by writing a copy of the data file with selected keyword
+values removed.  
+
+DeID has been revised (July 2013) to enable processing of multi-block
+data files.
diff --git a/academic/wehi-deid/doinst.sh b/academic/wehi-deid/doinst.sh
new file mode 100644
index 0000000000..5fb28930db
--- /dev/null
+++ b/academic/wehi-deid/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/wehi-deid/slack-desc b/academic/wehi-deid/slack-desc
new file mode 100644
index 0000000000..8f3033ef36
--- /dev/null
+++ b/academic/wehi-deid/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------------------------------------------------------|
+wehi-deid: wehi-deid (Flow cytometry De-Identifier)
+wehi-deid:
+wehi-deid: Where flow cytometry data files from the clinic are to be used in
+wehi-deid: research projects, DeID is used to remove patient identification.
+wehi-deid: This is achieved by writing a copy of the data file with selected
+wehi-deid: keyword values removed.
+wehi-deid:
+wehi-deid: Home: http://www.frankbattye.com.au/freesoftware.html
+wehi-deid:
+wehi-deid:
+wehi-deid:
diff --git a/academic/wehi-deid/wehi-deid.SlackBuild b/academic/wehi-deid/wehi-deid.SlackBuild
new file mode 100644
index 0000000000..af6a31c284
--- /dev/null
+++ b/academic/wehi-deid/wehi-deid.SlackBuild
@@ -0,0 +1,58 @@
+#!/bin/sh
+
+# Slackware build script for wehi-deid
+
+# 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=wehi-deid
+VERSION=${VERSION:-20130720}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+ARCH=noarch
+SRCNAM=DeID
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+
+install -D -m755 $CWD/$SRCNAM.jar $PKG/usr/bin/$PRGNAM.jar
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
+
+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/wehi-deid/wehi-deid.desktop b/academic/wehi-deid/wehi-deid.desktop
new file mode 100644
index 0000000000..4c6f5527d1
--- /dev/null
+++ b/academic/wehi-deid/wehi-deid.desktop
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Type=Application
+Exec=java -jar /usr/bin/wehi-deid.jar
+Terminal=false
+Name=Flow cytometry DeID
+Comment=Flow cytometry De-Identifier
+Icon=wehi-deid.png
+Categories=Education;
diff --git a/academic/wehi-deid/wehi-deid.info b/academic/wehi-deid/wehi-deid.info
new file mode 100644
index 0000000000..ce613b6662
--- /dev/null
+++ b/academic/wehi-deid/wehi-deid.info
@@ -0,0 +1,10 @@
+PRGNAM="wehi-deid"
+VERSION="20130720"
+HOMEPAGE="http://www.frankbattye.com.au/freesoftware.html"
+DOWNLOAD="http://www.frankbattye.com.au/downloads/DeID.jar"
+MD5SUM="bd938d07b0471cf9ed9f32b778ded63d"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="jdk"
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/wehi-deid/wehi-deid.png b/academic/wehi-deid/wehi-deid.png
new file mode 100644
index 0000000000..3699088e53
--- /dev/null
+++ b/academic/wehi-deid/wehi-deid.png