diff options
Diffstat (limited to 'academic/aliview')
-rw-r--r-- | academic/aliview/README | 39 | ||||
-rw-r--r-- | academic/aliview/aliview.SlackBuild | 82 | ||||
-rw-r--r-- | academic/aliview/aliview.desktop | 7 | ||||
-rw-r--r-- | academic/aliview/aliview.info | 10 | ||||
-rw-r--r-- | academic/aliview/doinst.sh | 3 | ||||
-rw-r--r-- | academic/aliview/slack-desc | 19 |
6 files changed, 160 insertions, 0 deletions
diff --git a/academic/aliview/README b/academic/aliview/README new file mode 100644 index 0000000000000..d9e65dc923e6a --- /dev/null +++ b/academic/aliview/README @@ -0,0 +1,39 @@ +AliView is yet another alignment viewer and editor, but this is +probably one of the fastest and most intuitive to use. Features: + +- fast and light-weight +- simple navigation, mouse-wheel zoom out and zoom in +- highlight consensus characters or characters deviating +- edit sequences/alignment (manually) +- align, add and align automatically with any aligner of your choice +- align new sequences to existing or realign all +- realign a selected block +- realign nucleotides as translated amino-acids +- delete vertical gaps +- undo/redo +- find degenerate primers in conserved regions in an alignment +- open and save in FASTA, NEXUS, PHYLIP, CLUSTAL or MSF format +- print (current view) +- export whole alignment as an image file (png-format) +- copy selection (as fasta-sequences or just characters) +- paste sequences (as sequences or filenames) +- add more sequences from file +- merge two sequences - and calculate consensus +- translate (view) nucleotide sequences as amino-acid sequences +- save translated alignment +- read / preserve Codonpos, Charset and Excludes (Nexus-specification) +- change Codonpos for selected regions (Nexus-specification) +- drag-drop/remove of sequences/files +- move sequences to top/bottom with key-stroke +- a simple "external interface" that lets you invoke other programs +- search function that finds patterns across gaps and follows IUPAC +- search multiple sequence names at once (stored in clipboard) +- reverse complement/reverse/complement sequences or whole alignment +- different color schemes +- sort sequences by name +- sort sequences by residue in selected column + +Citation: +Larsson, A. (2014). AliView: a fast and lightweight alignment viewer +and editor for large data sets. Bioinformatics30(22): 3276-3278. +http://dx.doi.org/10.1093/bioinformatics/btu531 diff --git a/academic/aliview/aliview.SlackBuild b/academic/aliview/aliview.SlackBuild new file mode 100644 index 0000000000000..12f023916deeb --- /dev/null +++ b/academic/aliview/aliview.SlackBuild @@ -0,0 +1,82 @@ +#!/bin/sh + +# Slackware build script for aliview + +# Copyright 2018 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=aliview +VERSION=${VERSION:-1.21} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +ARCH=noarch + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM.tgz +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 the jar file of AliView +mkdir -p $PKG/usr/share/$PRGNAM +cp $PRGNAM.jar $PKG/usr/share/$PRGNAM + +# Install the wrapper provided by the author +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM + +# Let's use our own .desktop file +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp aliicon_128x128.png $PKG/usr/share/pixmaps/$PRGNAM.png + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a install.readme.txt README.txt $PKG/usr/doc/$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:-tgz} diff --git a/academic/aliview/aliview.desktop b/academic/aliview/aliview.desktop new file mode 100644 index 0000000000000..705345a204c91 --- /dev/null +++ b/academic/aliview/aliview.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=aliview +Icon=aliview +Name=AliView +StartupNotify=false +Type=Application diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info new file mode 100644 index 0000000000000..f4241366de6a7 --- /dev/null +++ b/academic/aliview/aliview.info @@ -0,0 +1,10 @@ +PRGNAM="aliview" +VERSION="1.21" +HOMEPAGE="http://www.ormbunkar.se/aliview/" +DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-version-1.21/aliview.tgz" +MD5SUM="9b04979a88a5cae94d9b1580e9aa2f7a" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/aliview/doinst.sh b/academic/aliview/doinst.sh new file mode 100644 index 0000000000000..5fb28930db0b9 --- /dev/null +++ b/academic/aliview/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/aliview/slack-desc b/academic/aliview/slack-desc new file mode 100644 index 0000000000000..6f9c46c189728 --- /dev/null +++ b/academic/aliview/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------------------------------------------------------| +aliview: aliview (Alignment viewer and editor) +aliview: +aliview: AliView is yet another alignment viewer and editor, but this is +aliview: probably one of the fastest and most intuitive to use. +aliview: +aliview: http://www.ormbunkar.se/aliview/ +aliview: +aliview: +aliview: +aliview: +aliview: |