From aba0ae57532c359093a9727094bfbbfa3074ede1 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 27 Jan 2014 22:20:11 +0700 Subject: academic/amplifx: Added (Manage, test and design your primers). Signed-off-by: Willy Sudiarto Raharjo --- academic/amplifx/README | 37 ++++++++++++++++++ academic/amplifx/References | 2 + academic/amplifx/amplifx | 3 ++ academic/amplifx/amplifx.SlackBuild | 75 ++++++++++++++++++++++++++++++++++++ academic/amplifx/amplifx.desktop | 7 ++++ academic/amplifx/amplifx.info | 10 +++++ academic/amplifx/amplifx.png | Bin 0 -> 14038 bytes academic/amplifx/doinst.sh | 4 ++ academic/amplifx/slack-desc | 19 +++++++++ 9 files changed, 157 insertions(+) create mode 100644 academic/amplifx/README create mode 100644 academic/amplifx/References create mode 100644 academic/amplifx/amplifx create mode 100644 academic/amplifx/amplifx.SlackBuild create mode 100644 academic/amplifx/amplifx.desktop create mode 100644 academic/amplifx/amplifx.info create mode 100644 academic/amplifx/amplifx.png create mode 100644 academic/amplifx/doinst.sh create mode 100644 academic/amplifx/slack-desc (limited to 'academic/amplifx') diff --git a/academic/amplifx/README b/academic/amplifx/README new file mode 100644 index 0000000000..c5394bb809 --- /dev/null +++ b/academic/amplifx/README @@ -0,0 +1,37 @@ +AmplifX: Manage, test and design your primers for PCR. + +The main purpose of AmplifX is to seek in a collection of primers, +such as any molecular biologist get in his refrigerators, those which +can be use to amplify a fragment into a target sequence, for example, +and particularly, to design strategies to screen recombinant clones by +PCR. Main features: + +Manage your primers +- Import or easily create primer lists +- Name,comment, sort primers +- Share simply primer lists (automatic lockout in read only mode of + files yet opened by an other user) +- Automatic calculation of quality score (TM [Santa-Lucia method], + length, GC%, autodimer, complexity, etc.) +- Works with degenerate sequences + +Test your primers +- Localise your primers on target sequences (main file formats + supported and "intelligent" copy-paste) +- Prediction of amplified sequences +- Interactive graphic map +- Pertinent informations on matches and amplicons (TM, size, predicted + dimers, etc.) + +Design your primers +- Simple and intuitive interface to design new primers for amplifying + a fragment choosing the amplicon size and/or the position +- Many of design options + +NOTE: +This is just repackaging of the ready binary for x86 and will not run +on x86_64. It will probably work fine on a Slackware multilib box. + +How to cite AmplifX: +AmplifX X.X.X [version number] by Nicolas Jullien; CNRS, Aix-Marseille +Université - http://crn2m.univ-mrs.fr/pub/amplifx-dist diff --git a/academic/amplifx/References b/academic/amplifx/References new file mode 100644 index 0000000000..141ef9025b --- /dev/null +++ b/academic/amplifx/References @@ -0,0 +1,2 @@ +AmplifX X.X.X [version number] by Nicolas Jullien; CNRS, Aix-Marseille +Université - http://crn2m.univ-mrs.fr/pub/amplifx-dist diff --git a/academic/amplifx/amplifx b/academic/amplifx/amplifx new file mode 100644 index 0000000000..0feceb046b --- /dev/null +++ b/academic/amplifx/amplifx @@ -0,0 +1,3 @@ +#!/bin/sh +cd /opt/amplifx +./AmplifX & diff --git a/academic/amplifx/amplifx.SlackBuild b/academic/amplifx/amplifx.SlackBuild new file mode 100644 index 0000000000..b1b82d6e69 --- /dev/null +++ b/academic/amplifx/amplifx.SlackBuild @@ -0,0 +1,75 @@ +#!/bin/sh + +# Slackware build script for amplifx + +# Copyright 2014 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=amplifx +SRCNAM=AmplifX_Lin_Latest +VERSION=${VERSION:-1.7.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +ARCH=i386 + +CWD=$(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 +unzip $CWD/$SRCNAM.zip +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 {} \; + +# Put things in /opt, as the binary expects the libraries folder to be +# in its current location. +mkdir -p $PKG/opt/$PRGNAM +cp -a ./AmplifX/* $PKG/opt/$PRGNAM + +# This is a simple wrapper to go in /usr/bin +install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM + +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 $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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/amplifx/amplifx.desktop b/academic/amplifx/amplifx.desktop new file mode 100644 index 0000000000..dfc4d33550 --- /dev/null +++ b/academic/amplifx/amplifx.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=amplifx +Icon=amplifx +Name=AmplifX +StartupNotify=false +Type=Application diff --git a/academic/amplifx/amplifx.info b/academic/amplifx/amplifx.info new file mode 100644 index 0000000000..72fe05f382 --- /dev/null +++ b/academic/amplifx/amplifx.info @@ -0,0 +1,10 @@ +PRGNAM="amplifx" +VERSION="1.7.0" +HOMEPAGE="http://crn2m.univ-mrs.fr/AmplifX" +DOWNLOAD="http://crn2m.univ-mrs.fr/IMG/zip/AmplifX_Lin_Latest.zip" +MD5SUM="ff84d1c4a800dcb651beaa877ff7b1ca" +DOWNLOAD_x86_64="UNSUPPORTED" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/amplifx/amplifx.png b/academic/amplifx/amplifx.png new file mode 100644 index 0000000000..f764b6458a Binary files /dev/null and b/academic/amplifx/amplifx.png differ diff --git a/academic/amplifx/doinst.sh b/academic/amplifx/doinst.sh new file mode 100644 index 0000000000..4e8ba7071d --- /dev/null +++ b/academic/amplifx/doinst.sh @@ -0,0 +1,4 @@ +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/amplifx/slack-desc b/academic/amplifx/slack-desc new file mode 100644 index 0000000000..60d74ca6e9 --- /dev/null +++ b/academic/amplifx/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------------------------------------------------------| +amplifx: amplifx: (Manage, test and design your primers for PCR) +amplifx: +amplifx: The main purpose of AmplifX is to seek in a collection of primers, +amplifx: such as any molecular biologist get in his refrigerators, those +amplifx: which can be use to amplify a fragment into a target sequence, +amplifx: for example, and particularly, to design strategies to screen +amplifx: recombinant clones by PCR. +amplifx: +amplifx: Home: http://crn2m.univ-mrs.fr/AmplifX +amplifx: References: /usr/doc/amplifx-1.7.0/References +amplifx: -- cgit v1.2.3-65-gdbad