academic/FigTree: Add (A graphical viewer of phylogenetic trees).

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

6 files changed, 118 insertions, 0 deletions

diff --git a/academic/FigTree/FigTree.SlackBuild b/academic/FigTree/FigTree.SlackBuild
new file mode 100644
index 000000000000..f70e42ca9ab2
--- /dev/null
+++ b/academic/FigTree/FigTree.SlackBuild
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+# Slackware build script for FigTree
+
+# Copyright 2023 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.
+
+cd $(dirname $0) ; CWD=$(pwd)
+
+PRGNAM=FigTree
+VERSION=${VERSION:-1.4.4}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+ARCH=noarch
+
+if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
+  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
+  exit 0
+fi
+
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf ${PRGNAM}_v${VERSION}
+tar xvf $CWD/${PRGNAM}_v${VERSION}.tgz
+cd ${PRGNAM}_v${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 {} \;
+
+install -D -m 755 bin/figtree $PKG/usr/bin/figtree
+install -D -m 644 lib/figtree.jar $PKG/usr/share/$PRGNAM/figtree.jar
+install -D -m 644 images/figtree.png $PKG/usr/share/pixmaps/figtree.png
+install -D -m 644 $CWD/FigTree.desktop $PKG/usr/share/applications/FigTree.desktop
+
+sed -i "s:-Xmx512m:-Xmx1024m:" $PKG/usr/bin/figtree
+sed -i "s:lib:/usr/share/$PRGNAM:" $PKG/usr/bin/figtree
+
+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
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
diff --git a/academic/FigTree/FigTree.desktop b/academic/FigTree/FigTree.desktop
new file mode 100644
index 000000000000..1b20f2067f5e
--- /dev/null
+++ b/academic/FigTree/FigTree.desktop
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Name=FigTree
+Comment=Phylogenetic Viewer
+Exec=figtree
+Icon=figtree
+StartupNotify=false
+Type=Application
+Categories=Education
diff --git a/academic/FigTree/FigTree.info b/academic/FigTree/FigTree.info
new file mode 100644
index 000000000000..eb72999634e7
--- /dev/null
+++ b/academic/FigTree/FigTree.info
@@ -0,0 +1,10 @@
+PRGNAM="FigTree"
+VERSION="1.4.4"
+HOMEPAGE="http://tree.bio.ed.ac.uk/software/figtree/"
+DOWNLOAD="https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree_v1.4.4.tgz"
+MD5SUM="7039dbb6109c66512599a1ae7b972be6"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="zulu-openjdk8"
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/FigTree/README b/academic/FigTree/README
new file mode 100644
index 000000000000..f80a4534f32f
--- /dev/null
+++ b/academic/FigTree/README
@@ -0,0 +1,3 @@
+FigTree is designed as a graphical viewer of phylogenetic trees and as a
+program for producing publication-ready figures. It can display
+summarized and annotated trees produced by BEAST.
diff --git a/academic/FigTree/doinst.sh b/academic/FigTree/doinst.sh
new file mode 100644
index 000000000000..5fb28930db0b
--- /dev/null
+++ b/academic/FigTree/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/FigTree/slack-desc b/academic/FigTree/slack-desc
new file mode 100644
index 000000000000..27bc500ce7af
--- /dev/null
+++ b/academic/FigTree/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------------------------------------------------------|
+FigTree: FigTree (A graphical viewer of phylogenetic trees)
+FigTree:
+FigTree: FigTree is designed as a graphical viewer of phylogenetic trees
+FigTree: and as a program for producing publication-ready figures. 
+FigTree:
+FigTree: http://tree.bio.ed.ac.uk/software/figtree/
+FigTree:
+FigTree:
+FigTree:
+FigTree:
+FigTree: