From d2c42f9118a01a2164bdf11c406986b7f3a95811 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sat, 6 Jul 2013 01:22:06 -0500 Subject: academic/jalview: Added (A Sequence Alignment Editor and Viewer) Signed-off-by: Robby Workman --- academic/jalview/README | 16 +++++++ academic/jalview/References | 28 +++++++++++++ academic/jalview/doinst.sh | 3 ++ academic/jalview/jalview | 16 +++++++ academic/jalview/jalview.SlackBuild | 81 ++++++++++++++++++++++++++++++++++++ academic/jalview/jalview.desktop | 8 ++++ academic/jalview/jalview.info | 12 ++++++ academic/jalview/jalview.png | Bin 0 -> 2471 bytes academic/jalview/slack-desc | 19 +++++++++ 9 files changed, 183 insertions(+) create mode 100644 academic/jalview/README create mode 100644 academic/jalview/References create mode 100644 academic/jalview/doinst.sh create mode 100644 academic/jalview/jalview create mode 100644 academic/jalview/jalview.SlackBuild create mode 100644 academic/jalview/jalview.desktop create mode 100644 academic/jalview/jalview.info create mode 100644 academic/jalview/jalview.png create mode 100644 academic/jalview/slack-desc diff --git a/academic/jalview/README b/academic/jalview/README new file mode 100644 index 0000000000..abb473680a --- /dev/null +++ b/academic/jalview/README @@ -0,0 +1,16 @@ +Jalview - A Sequence Alignment Editor and Viewer + +Jalview is a free program developed for the interactive editing, +analysis and visualization of multiple sequence alignments (MSA). It +can also work with sequence annotation, secondary structure +information, phylogenetic trees and 3D molecular structures. + +If you use Jalview 2 in your work, please cite: +Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) +Jalview Version 2-a multiple sequence alignment editor and analysis +workbench. Bioinformatics 25: 1189-1191. + +NOTE: +The silly requirement of p7zip is just for extracting the program's +contents at build time. You do not need it in order to use Jalview +later on, but it's a nice tool to have anyways... ;) diff --git a/academic/jalview/References b/academic/jalview/References new file mode 100644 index 0000000000..bb4030f270 --- /dev/null +++ b/academic/jalview/References @@ -0,0 +1,28 @@ +Peer reviewed publications + +If you use Jalview 2 in your work, please cite Waterhouse et al. +(2009). +To cite an analysis performed with JABAWS, please use Troshin et al. +(2011). + +Troshin PV, Procter JB, Barton GJ (2011) Java bioinformatics analysis +web services for multiple sequence alignment--JABAWS:MSA. +Bioinformatics 27: 2001-2002. +http://bioinformatics.oxfordjournals.org/content/27/14/2001 + +Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) +Jalview Version 2-a multiple sequence alignment editor and analysis +workbench. Bioinformatics 25: 1189-1191. +http://bioinformatics.oxfordjournals.org/content/25/9/1189 + +Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, et al. +(2006) MACSIMS: multiple alignment of complete sequences information +management system. BMC Bioinformatics 7: 318. +http://www.biomedcentral.com/1471-2105/7/318 + +Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java +alignment editor. Bioinformatics 20: 426-427. +http://bioinformatics.oxfordjournals.org/content/20/3/426 + +Take a look at the citations for the Jalview 2 paper in PubMedCentral: +http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=19151095 diff --git a/academic/jalview/doinst.sh b/academic/jalview/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/jalview/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/jalview/jalview b/academic/jalview/jalview new file mode 100644 index 0000000000..31813c2c2a --- /dev/null +++ b/academic/jalview/jalview @@ -0,0 +1,16 @@ +#!/bin/sh + +# This wrapper script is taken from Arch Linux AUR entry of jalview. +# https://aur.archlinux.org/packages/jalview/ +# Maintainer of the PKGBUILD is Stefan Seemayer. + +progname="jalview" +mainclass="jalview.bin.Jalview" +basedir="/usr/share/java/$progname" + +# build classpath: all jars in $basedir +cp=$( ls $basedir/*.jar | xargs echo | sed "s/ /:/g" ); + + +# run jar +"$JAVA_HOME/bin/java" -cp $cp $mainclass diff --git a/academic/jalview/jalview.SlackBuild b/academic/jalview/jalview.SlackBuild new file mode 100644 index 0000000000..101b9b7bf3 --- /dev/null +++ b/academic/jalview/jalview.SlackBuild @@ -0,0 +1,81 @@ +#!/bin/sh + +# Slackware build script for jalview + +# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# With help from the jalview PKGBUILD at Arch linux AUR: +# https://aur.archlinux.org/packages/jalview/ + +PRGNAM=jalview +VERSION=${VERSION:-2.8} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=install.bin +ARCH=noarch + +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 $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +7z e $CWD/$SRCNAM +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +mkdir -p $PKG/usr/share/java/$PRGNAM +cp -a *.jar $PKG/usr/share/java/$PRGNAM + +# The wrapper is from Arch. Thank you! +install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + building.html exampleFeatures.txt LICENSE README_IA \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/TheJalviewTutorial_screen.pdf > $PKG/usr/doc/$PRGNAM-$VERSION/Tutorial.pdf +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Menu item and icon +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/jalview/jalview.desktop b/academic/jalview/jalview.desktop new file mode 100644 index 0000000000..bfc8d516f5 --- /dev/null +++ b/academic/jalview/jalview.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Name=Jalview +Comment=A Sequence Alignment Editor and Viewer +Exec=jalview +Icon=jalview +StartupNotify=false +Type=Application +Categories=Education; diff --git a/academic/jalview/jalview.info b/academic/jalview/jalview.info new file mode 100644 index 0000000000..29b7a3356c --- /dev/null +++ b/academic/jalview/jalview.info @@ -0,0 +1,12 @@ +PRGNAM="jalview" +VERSION="2.8" +HOMEPAGE="http://www.jalview.org/" +DOWNLOAD="http://www.jalview.org/Web_Installers/InstData/Linux/NoVM/install.bin \ + http://www.jalview.org/tutorial/TheJalviewTutorial_screen.pdf" +MD5SUM="8efc117dc7947b24577b319ffdadb024 \ + e08a446029df593d2e2722c5f273ce6c" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk p7zip" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/jalview/jalview.png b/academic/jalview/jalview.png new file mode 100644 index 0000000000..56dcdcaf99 Binary files /dev/null and b/academic/jalview/jalview.png differ diff --git a/academic/jalview/slack-desc b/academic/jalview/slack-desc new file mode 100644 index 0000000000..3d6bb1f727 --- /dev/null +++ b/academic/jalview/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------------------------------------------------------| +jalview: jalview (A Sequence Alignment Editor and Viewer) +jalview: +jalview: Jalview is a free program developed for the interactive editing, +jalview: analysis and visualization of multiple sequence alignments (MSA). +jalview: It can also work with sequence annotation, secondary structure +jalview: information, phylogenetic trees and 3D molecular structures. +jalview: +jalview: Home: http://www.jalview.org/ +jalview: References: /usr/doc/jalview-$VERSION/References +jalview: +jalview: -- cgit v1.2.3