From a536adc58ea490c6f96545506d8c8d22fbaacc98 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 30 Jun 2013 15:15:05 -0500 Subject: [PATCH] academic/aline: Added (Tk graphical interface for Perl) Signed-off-by: Erik Hanson --- academic/aline/README | 16 +++++++ academic/aline/References | 4 ++ academic/aline/aline.SlackBuild | 82 ++++++++++++++++++++++++++++++++ academic/aline/aline.desktop | 8 ++++ academic/aline/aline.info | 10 ++++ academic/aline/aline.png | Bin 0 -> 1399 bytes academic/aline/doinst.sh | 3 ++ academic/aline/slack-desc | 19 ++++++++ 8 files changed, 142 insertions(+) create mode 100644 academic/aline/README create mode 100644 academic/aline/References create mode 100644 academic/aline/aline.SlackBuild create mode 100644 academic/aline/aline.desktop create mode 100644 academic/aline/aline.info create mode 100644 academic/aline/aline.png create mode 100644 academic/aline/doinst.sh create mode 100644 academic/aline/slack-desc diff --git a/academic/aline/README b/academic/aline/README new file mode 100644 index 0000000000..28549e30b4 --- /dev/null +++ b/academic/aline/README @@ -0,0 +1,16 @@ +Aline: An Extensible WYSIWYG Protein Sequence Alignment Editor for +Publication Quality Figures. + +Aline is an interactive perl/tk application which can read common +sequence alignment formats which the user can then alter, embellish, +markup etc to produce the kind of sequence figure commonly found in +biochemical articles. + +Please cite: +Bond, C.S. and Schüttelkopf, A.W. (2009), Acta cryst. D65, 510-512 + +NOTE: +Although not needed for running Aline, clustalw and mkDSSP are +desirable for its complete functionality. A third tool is CHAINSAW, +part of the CCP4 suite (http://www.ccp4.ac.uk/). Visit the web site +for more information and installation instructions if you want it. diff --git a/academic/aline/References b/academic/aline/References new file mode 100644 index 0000000000..9deaad773d --- /dev/null +++ b/academic/aline/References @@ -0,0 +1,4 @@ +Please cite +Bond, C.S. and Schüttelkopf, A.W. (2009), Acta cryst. +D65, 510-512 +http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/actad_65_510.pdf diff --git a/academic/aline/aline.SlackBuild b/academic/aline/aline.SlackBuild new file mode 100644 index 0000000000..433c1bbc61 --- /dev/null +++ b/academic/aline/aline.SlackBuild @@ -0,0 +1,82 @@ +#!/bin/sh + +# Slackware build script for aline + +# 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. + +PRGNAM=aline +VERSION=${VERSION:-1.0.025} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCVER=011208 +ARCH=noarch + +CWD=$(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 ${PRGNAM}_${SRCVER} +tar xvf $CWD/${PRGNAM}_${SRCVER}.tar.gz +cd ${PRGNAM}_${SRCVER} +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 {} \; + +# Point aline to the correct paths of its colour schemes, examples, +# plugins and scripts. +sed -i "s:%%SELFcolourschemes:/usr/share/$PRGNAM/colourschemes:g" bin/aline +sed -i "s:%%SELFexample:/usr/share/$PRGNAM/example:g" bin/aline +sed -i "s:%%SELFplugins:/usr/share/$PRGNAM/plugins:g" bin/aline +sed -i "s:%%SELFscripts:/usr/share/$PRGNAM/scripts:g" bin/aline + +install -D -m755 bin/$PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 bin/convertdump $PKG/usr/bin/convertdump + +mkdir -p $PKG/usr/share/$PRGNAM/ +cp -a \ +colourschemes example plugins \ + $PKG/usr/share/$PRGNAM/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Couldn't find an icon, so I assembled this thing from the program's logo... +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.${PKGTYPE:-tgz} diff --git a/academic/aline/aline.desktop b/academic/aline/aline.desktop new file mode 100644 index 0000000000..d19db01cca --- /dev/null +++ b/academic/aline/aline.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Name=Aline +Comment=A Protein Sequence Alignment Editor +Exec=aline +Icon=aline +StartupNotify=false +Type=Application +Categories=Education; diff --git a/academic/aline/aline.info b/academic/aline/aline.info new file mode 100644 index 0000000000..569ad088d0 --- /dev/null +++ b/academic/aline/aline.info @@ -0,0 +1,10 @@ +PRGNAM="aline" +VERSION="1.0.025" +HOMEPAGE="http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/" +DOWNLOAD="http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/aline_011208.tar.gz" +MD5SUM="6e462b37bb016de731a3352cc9503cd9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="perl-tk" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/aline/aline.png b/academic/aline/aline.png new file mode 100644 index 0000000000000000000000000000000000000000..a6b212a244375534b738fccdfc5ba91c72bc0cbb GIT binary patch literal 1399 zcmV--1&I2IP)ZB z0j(N?p%LGR+4y37fi1jL1QJMyK4_FG5=ulQid+hI7u%ZFR=QijX<>WYl1R3cLg;O2 zJ3cHuI@wG2GHoI0FPY?=?|k3R|G#tQp+f)|-^}-EU>KdZU{B92thN$W?B>m@SZ&9&QK=zb4Ond@+_}>Z zz?|93Mcm=29vf9b;MIV`@uz6#t>4Yuxi155V|VY~7#n2);$gt)l*RN(NzP&Z{8gkR zX9LjP?ev&hav zuRl)vjoPtOI0C9=w4w0~*X)9ovuPy*oSD>Y(T(qO2rVtxD zQ*}s^JN<9@6pAu5wn}{!I8nCmWi#B0C&O0%Vc6Is9 z5eA-5-AGcRd$oyb==*5y$sMATN9or2-*P1OYn9a=q zI~7GK3{`{A?R22%bP^_0mPhvS9;Z5w-ze{88D)-hCAS z#Kc5;8qf%@yU|C92?OKJgn{v9!oYYlVPL#@Ej}i7i_)0GK-UvC%pW5n;aG zHVh6bWM>x#UD(vzDSjgy4H6Lge)=ImOretd2T@SC-!~uzBPU0q)BX3{JK!2*z~vsF z6cxcwyU%fS`_B;Ko?en9<&y=^QIwhvfNN+7*O2eG9ePP3TCWFS|8<#_gj9hM~?3+q9@7_3;x;Wx!!P24r^%rESPgtoqTEmp5VzgE1hlR0ISQV-G$x?U+=@5S zDf>G758A=t?Is4ev?fp056Hj^d8y/dev/null 2>&1 +fi diff --git a/academic/aline/slack-desc b/academic/aline/slack-desc new file mode 100644 index 0000000000..61662e1715 --- /dev/null +++ b/academic/aline/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------------------------------------------------------| +aline: aline (A Sequence Alignment Editor and Viewer) +aline: +aline: Aline: An Extensible WYSIWYG Protein Sequence Alignment Editor +aline: Publication Quality Figures. Aline is an interactive perl/tk +aline: application which can read common sequence alignment formats +aline: which the user can then alter, embellish, markup etc to produce +aline: the kind of sequence figure commonly found in biochemical articles. +aline: +aline: Home: http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ +aline: References: /usr/doc/aline-$VERSION/References +aline: