academic/trfind: Added (Tandem repeats finder: analyze DNA seqs).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
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057d020475
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79d1caba14
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Tandem Repeats Finder License Terms
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The author of this software grants to any individual or organization the
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right to use and to make an unlimited number of copies of this software.
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You may not de-compile, disassemble, reverse engineer, or modify the
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software. This software cannot be sold, incorporated into commercial
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software or redistributed. The author of this software accepts no
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responsibility for damages resulting from the use of this software and
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makes no warranty or representation, either express or implied,
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including but not limited to, any implied warranty of merchantability or
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fitness for a particular purpose. This software is provided as is, and
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the user assumes all risks when using it.
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Tandem repeats finder: a program to analyze DNA sequences
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A tandem repeat in DNA is two or more adjacent, approximate copies of a
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pattern of nucleotides. Tandem Repeats Finder is a program to locate and
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display tandem repeats in DNA sequences. In order to use the program,
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the user submits a sequence in FASTA format.
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Example usage:
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trf hg38.fasta 2 5 7 80 10 50 2000 -l 6
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LICENSE:
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Please read the License Terms before downloading:
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https://tandem.bu.edu/trf/trf.license.html
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Please cite:
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G. Benson "Tandem repeats finder: a program to analyze DNA sequences"
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Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.
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Please cite:
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G. Benson,
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"Tandem repeats finder: a program to analyze DNA sequences"
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Nucleic Acids Research (1999)
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Vol. 27, No. 2, pp. 573-580.
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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trfind: trfind (Tandem repeats finder: a program to analyze DNA sequences)
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trfind:
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trfind: Tandem Repeats Finder is a program to locate and display tandem
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trfind: repeats in DNA sequences.
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trfind:
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trfind: Home: https://tandem.bu.edu/trf/trf.html
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trfind:
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trfind:
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trfind:
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trfind:
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trfind:
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#!/bin/sh
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# Slackware build script for trfind
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# Copyright 2018 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=trfind
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VERSION=${VERSION:-4.09}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCNAM=trf
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BINVER=409
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i386 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n"
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exit 1
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fi
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# Determine binary architecture
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if [ "$ARCH" = "x86_64" ]; then
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BINARCH="linux64"
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else
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BINARCH="linux32"
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fi
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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install -D -m755 $CWD/${SRCNAM}${BINVER}.${BINARCH} $PKG/usr/bin/$PRGNAM
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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PRGNAM="trfind"
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VERSION="4.09"
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HOMEPAGE="https://tandem.bu.edu/trf/trf.html"
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DOWNLOAD="http://tandem.bu.edu/trf/downloads/trf409.linux32"
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MD5SUM="285478f16f417d6e9c9700f556373e43"
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DOWNLOAD_x86_64="http://tandem.bu.edu/trf/downloads/trf409.linux64"
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MD5SUM_x86_64="0c594fe666e0332db1df9d160d7fabc8"
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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