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academic/sequence-analysis: Updated for version 1.7.2.

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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Petar Petrov 2015-11-11 23:09:52 +07:00 committed by Willy Sudiarto Raharjo
parent 49c8bb6b8f
commit 9177640ee4
3 changed files with 46 additions and 12 deletions
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19
academic/sequence-analysis/README
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A collage of coding projects for biologic sequences analysis.
The upper window panel can hold several sequences, which are both
editable and selectable. The tabs in the lower analysis panel try to
keep up with the current sequence selection to provide immediate
feedback. The selection is used in some modules as only the portion
being analyzed for other modules i.e. Digest is used to determine if
enzymes cut in the in or outside of the selection.
Most commonly available sequence formats have been reverse engineered.
You can also access a sequences from the NCBI via its GID or UID. This
currently cannot be done from behind a firewall.
Most of the analyses are simple enough that they are obvious to use,
Composition, pI. Others could stand some documenation i.e. Pairwise
and Primer Design. The Publish tab uses a string to control the
layout. Click on the Legend button for some help.
NOTE:
The 'source' is hosted at SourceForge by the SlackBuild maintainer.

31
academic/sequence-analysis/sequence-analysis.SlackBuild
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#!/bin/sh
# Slackware build script for sequence-analysis
# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
# hereby submitted to the public domain
# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
# Copyright 2011-2015 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=sequence-analysis
VERSION=${VERSION:-1.6.0}
ARCH=noarch
BUILD=${BUILD:-2}
VERSION=${VERSION:-1.7.2}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
ARCH=noarch
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM

8
academic/sequence-analysis/sequence-analysis.info
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PRGNAM="sequence-analysis"
VERSION="1.6.0"
VERSION="1.7.2"
HOMEPAGE="http://informagen.com/SA/"
DOWNLOAD="http://urchlay.naptime.net/~urchlay/src/sa.jar"
MD5SUM="48609bfdd0d689cc62467159a0308886"
DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/sequence-analysis/1.7.2/sa.jar"
MD5SUM="815c7e6a8717a9e2a7fedc9ed94fbd0e"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="jdk"
MAINTAINER="Petar Petrov"
EMAIL="ppetrov@paju.oulu.fi"
EMAIL="petar.petrov@student.oulu.fi"