academic/finchtv: Added (Brilliant Trace Viewer).

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

9 files changed, 245 insertions, 0 deletions

diff --git a/academic/finchtv/COMPANY b/academic/finchtv/COMPANY
new file mode 100644
index 000000000000..702989c3ce8d
--- /dev/null
+++ b/academic/finchtv/COMPANY
@@ -0,0 +1,51 @@
+About Geospiza (http://www.geospiza.com/Company/default.shtml)
+
+Geospiza is a leading developer of enterprise-class software systems
+for workflow management of genetic analysis.
+
+Geospiza has established itself as the life science industry’s top 
+software developer for meeting the combined laboratory, data 
+management and analytical needs of biotechnology and pharmaceutical 
+companies, universities, researchers, contract core and diagnostic 
+laboratories involved in genetic testing and manufacturing bio-
+therapeutics.
+
+The life sciences field is rapidly evolving beyond sequencing genomes 
+for pure research to developing clinically relevant initiatives such 
+as understanding what genetic information is useful for drug 
+development, determining drug efficacy, toxicity screening and 
+diagnosing infectious agents.
+
+This expansion of the field is resulting in a dramatic increase in the
+amount of data that must be managed by genetic testing laboratories 
+and research institutions. Underscoring this growth is the desire by 
+the Food & Drug Administration (FDA) and the broader healthcare 
+community to match drugs more specifically to a person's individual 
+genetic profile. The FDA is expected to focus on the sensitivity and 
+accuracy of these new diagnostics, thereby increasing the need for 
+verifiable, repeatable processes for testing.
+
+Today, the amount of manual work required to manage and make sense of 
+the vast amounts of genetic information being generated by clinical 
+and life science research laboratories worldwide is tremendous. In 
+order to be able to scale to meet this increased demand and scrutiny 
+in a cost-effective way, automated solutions are required.
+
+Geospiza makes software for crunching the vast amounts of genetic 
+data. When a laboratory uses GeneSifter Lab Edition, they are able to 
+significantly increase capacity, reduce their backlog, eliminate 
+errors due to manual processes, and speed time to discovery. The 
+software is being used today worldwide by leading institutions and 
+laboratories for everything from clinical DNA testing and bio-
+therapeutic manufacturing to contract core lab services and basic 
+research and discovery.
+
+Geospiza's products are designed and built by biologists, enabling 
+researchers to focus on the science, not the software.
+	
+
+More Information
+info.geospiza@perkinelmer.com
+Call (206) 633-4403.
+
+©Copyright 2013 PerkinElmer, Inc. All rights reserved. 
diff --git a/academic/finchtv/CONTACT b/academic/finchtv/CONTACT
new file mode 100644
index 000000000000..9aa4a571f09b
--- /dev/null
+++ b/academic/finchtv/CONTACT
@@ -0,0 +1,20 @@
+Contact (http://www.geospiza.com/Contact/default.shtml)
+
+Headquarters:
+Geospiza, Inc.
+100 West Harrison
+North Tower, Suite #330
+Seattle, WA 98119
+
+Phone: (206) 633-4403
+Fax: (206) 633-4415 	
+General Information
+info.geospiza@perkinelmer.com
+
+Product Information
+sales.geospiza@perkinelmer.com
+
+Technical Support
+gpz.support@perkinelemer.com
+
+©Copyright 2013 PerkinElmer, Inc. All rights reserved.
diff --git a/academic/finchtv/PRIVACY b/academic/finchtv/PRIVACY
new file mode 100644
index 000000000000..88acd6adfb4f
--- /dev/null
+++ b/academic/finchtv/PRIVACY
@@ -0,0 +1,42 @@
+Privacy Policy (http://www.geospiza.com/privacy.shtml)
+
+Geospiza requires customers who register to use its Services to 
+provide contact information, such as name, company name, address, 
+phone number, and e-mail address. At the time you express interest in
+attaining additional information, or when you register for a Service,
+we may also ask for additional personal information, such as title,
+department name, fax number, or additional company information as well
+as billing name and address, credit card number or purchase order
+number, and the number of users within the organization that will be
+using the Service.
+
+Geospiza uses the information that is collected to set up these
+accounts for individuals and their organizations. We may also use the
+information to contact customers to further discuss customer interest
+in our company, its Services, and to send information regarding our
+company or partners, such as promotions and events. Customers are
+invited to receive an email newsletter by providing an email address.
+Customer email addresses and any personal customer information will
+not be distributed or shared with third parties. Customers can opt out
+of being contacted by us, or receiving such information from us, at
+any time by sending an email to gpz.support@perkinelmer.com. 
+
+Separately, customers are also asked to provide an email address when
+registering for the Service, in order to receive a username and 
+password. We may also email information regarding updates to Services
+or company, and will send a Customer Newsletter. Again, email will not
+be distributed or shared and customers can opt out of receiving any 
+communication by emailing gpz.support@perkinelmer.com at the time it
+is distributed, or at the time any customer registers for a Service.
+
+Customers of the Service will be using the Service to host data and
+information ("Data"). Geospiza will not review, share, distribute,
+print, or reference any such Data except as provided in the Service’s
+Master Subscription Agreement, or as may be required by law.
+Individual records may at times be viewed or accessed only for the
+purpose of resolving a problem, support issue, or suspected violation
+of the Master Subscription Agreement, or as may be required by law.
+Of course, customers are responsible for maintaining the
+confidentiality and security of their user registration and password.
+
+©Copyright 2013 PerkinElmer, Inc. All rights reserved.
diff --git a/academic/finchtv/README b/academic/finchtv/README
new file mode 100644
index 000000000000..73c987e6d8a2
--- /dev/null
+++ b/academic/finchtv/README
@@ -0,0 +1,15 @@
+FinchTV - A Brilliant Trace Viewer
+
+Geospiza's FinchTV is the popular way to view DNA sequence traces.
+FinchTV started as the only chromatogram viewer that can display an
+entire trace in a scalable multi-pane view. And it leads the way with
+raw data views, BLAST searching and the ability to reverse complement
+sequences and traces.
+
+This is just repackaging of the ready i386 binary. It WILL work on a
+stock Slackware64 as well (no multilib needed).
+
+NOTE!
+This program is free, but you should REGISTER in order to get it.
+This means you have to use a web browser to download the "source"
+tarball.
diff --git a/academic/finchtv/doinst.sh b/academic/finchtv/doinst.sh
new file mode 100644
index 000000000000..5fb28930db0b
--- /dev/null
+++ b/academic/finchtv/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/finchtv/finchtv.SlackBuild b/academic/finchtv/finchtv.SlackBuild
new file mode 100644
index 000000000000..f758937d3b3a
--- /dev/null
+++ b/academic/finchtv/finchtv.SlackBuild
@@ -0,0 +1,77 @@
+#!/bin/sh
+
+# Slackware build script for finchtv
+
+# Copyright 2015  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=finchtv
+VERSION=${VERSION:-1.3.1}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+SRCVER=1_3_1
+ARCH=i386 # This will work on a stock Slackware64 as well.
+
+CWD=$(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 ${PRGNAM}_${SRCVER}
+tar xvf $CWD/${PRGNAM}_${SRCVER}.tar.gz
+cd ${PRGNAM}_${SRCVER}
+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 {} \;
+
+install -D -m755 $PRGNAM $PKG/usr/bin/$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 $PKG/usr/share/$PRGNAM
+cp -a SampleData $PKG/usr/share/$PRGNAM
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a Help License.txt ReleaseNotes.txt $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/COMPANY > $PKG/usr/doc/$PRGNAM-$VERSION/COMPANY
+cat $CWD/CONTACT > $PKG/usr/doc/$PRGNAM-$VERSION/CONTACT
+cat $CWD/PRIVACY > $PKG/usr/doc/$PRGNAM-$VERSION/PRIVACY
+
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+cp Help/media/FinchTV_Mac_App.png $PKG/usr/share/pixmaps/$PRGNAM.png
+
+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/finchtv/finchtv.desktop b/academic/finchtv/finchtv.desktop
new file mode 100644
index 000000000000..85c1a6411323
--- /dev/null
+++ b/academic/finchtv/finchtv.desktop
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Categories=Education;
+Exec=finchtv
+Icon=finchtv.png
+Name=FinchTV
+StartupNotify=false
+Type=Application
+GenericName=
diff --git a/academic/finchtv/finchtv.info b/academic/finchtv/finchtv.info
new file mode 100644
index 000000000000..97df56fc941c
--- /dev/null
+++ b/academic/finchtv/finchtv.info
@@ -0,0 +1,10 @@
+PRGNAM="finchtv"
+VERSION="1.3.1"
+HOMEPAGE="http://www.geospiza.com/Products/finchtv.shtml"
+DOWNLOAD="http://www.geospiza.com/Products/finchtvdlrequest.shtml"
+MD5SUM="bafea0b08c5348cbe745d1a4857948a4"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="petar.petrov@oulu.oulu.fi"
diff --git a/academic/finchtv/slack-desc b/academic/finchtv/slack-desc
new file mode 100644
index 000000000000..4b6e80d9cbec
--- /dev/null
+++ b/academic/finchtv/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------------------------------------------------------|
+finchtv: finchtv (A Brilliant Trace Viewer)
+finchtv:
+finchtv: Geospiza's FinchTV is the popular way to view DNA sequence traces.
+finchtv: FinchTV started as the only chromatogram viewer that can display
+finchtv: an entire trace in a scalable multi-pane view. And it leads the
+finchtv: way with raw data views, BLAST searching and the ability to reverse
+finchtv: complement sequences and traces.
+finchtv:
+finchtv: Home: http://www.geospiza.com/Products/finchtv.shtml
+finchtv:
+finchtv: