From 79d1caba144638334721eaa4fcc54942f45432dd Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 12 Jan 2018 21:51:40 +0000 Subject: academic/trfind: Added (Tandem repeats finder: analyze DNA seqs). Signed-off-by: David Spencer --- academic/trfind/LICENSE | 13 +++++++ academic/trfind/README | 17 +++++++++ academic/trfind/References | 5 +++ academic/trfind/slack-desc | 19 ++++++++++ academic/trfind/trfind.SlackBuild | 75 +++++++++++++++++++++++++++++++++++++++ academic/trfind/trfind.info | 10 ++++++ 6 files changed, 139 insertions(+) create mode 100644 academic/trfind/LICENSE create mode 100644 academic/trfind/README create mode 100644 academic/trfind/References create mode 100644 academic/trfind/slack-desc create mode 100644 academic/trfind/trfind.SlackBuild create mode 100644 academic/trfind/trfind.info (limited to 'academic') diff --git a/academic/trfind/LICENSE b/academic/trfind/LICENSE new file mode 100644 index 0000000000..b6b961ef0b --- /dev/null +++ b/academic/trfind/LICENSE @@ -0,0 +1,13 @@ +Tandem Repeats Finder License Terms + +The author of this software grants to any individual or organization the +right to use and to make an unlimited number of copies of this software. + +You may not de-compile, disassemble, reverse engineer, or modify the +software. This software cannot be sold, incorporated into commercial +software or redistributed. The author of this software accepts no +responsibility for damages resulting from the use of this software and +makes no warranty or representation, either express or implied, +including but not limited to, any implied warranty of merchantability or +fitness for a particular purpose. This software is provided as is, and +the user assumes all risks when using it. diff --git a/academic/trfind/README b/academic/trfind/README new file mode 100644 index 0000000000..000e646a2d --- /dev/null +++ b/academic/trfind/README @@ -0,0 +1,17 @@ +Tandem repeats finder: a program to analyze DNA sequences + +A tandem repeat in DNA is two or more adjacent, approximate copies of a +pattern of nucleotides. Tandem Repeats Finder is a program to locate and +display tandem repeats in DNA sequences. In order to use the program, +the user submits a sequence in FASTA format. + +Example usage: +trf hg38.fasta 2 5 7 80 10 50 2000 -l 6 + +LICENSE: +Please read the License Terms before downloading: +https://tandem.bu.edu/trf/trf.license.html + +Please cite: +G. Benson "Tandem repeats finder: a program to analyze DNA sequences" +Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580. diff --git a/academic/trfind/References b/academic/trfind/References new file mode 100644 index 0000000000..49e0e6cf56 --- /dev/null +++ b/academic/trfind/References @@ -0,0 +1,5 @@ +Please cite: +G. Benson, +"Tandem repeats finder: a program to analyze DNA sequences" +Nucleic Acids Research (1999) +Vol. 27, No. 2, pp. 573-580. diff --git a/academic/trfind/slack-desc b/academic/trfind/slack-desc new file mode 100644 index 0000000000..d94bdf10d2 --- /dev/null +++ b/academic/trfind/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------------------------------------------------------| +trfind: trfind (Tandem repeats finder: a program to analyze DNA sequences) +trfind: +trfind: Tandem Repeats Finder is a program to locate and display tandem +trfind: repeats in DNA sequences. +trfind: +trfind: Home: https://tandem.bu.edu/trf/trf.html +trfind: +trfind: +trfind: +trfind: +trfind: diff --git a/academic/trfind/trfind.SlackBuild b/academic/trfind/trfind.SlackBuild new file mode 100644 index 0000000000..0a177ec0d2 --- /dev/null +++ b/academic/trfind/trfind.SlackBuild @@ -0,0 +1,75 @@ +#!/bin/sh + +# Slackware build script for trfind + +# 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=trfind +VERSION=${VERSION:-4.09} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=trf +BINVER=409 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +# Determine binary architecture +if [ "$ARCH" = "x86_64" ]; then + BINARCH="linux64" +else + BINARCH="linux32" +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP + +install -D -m755 $CWD/${SRCNAM}${BINVER}.${BINARCH} $PKG/usr/bin/$PRGNAM + +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 +cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/trfind/trfind.info b/academic/trfind/trfind.info new file mode 100644 index 0000000000..2dfb07986d --- /dev/null +++ b/academic/trfind/trfind.info @@ -0,0 +1,10 @@ +PRGNAM="trfind" +VERSION="4.09" +HOMEPAGE="https://tandem.bu.edu/trf/trf.html" +DOWNLOAD="http://tandem.bu.edu/trf/downloads/trf409.linux32" +MD5SUM="285478f16f417d6e9c9700f556373e43" +DOWNLOAD_x86_64="http://tandem.bu.edu/trf/downloads/trf409.linux64" +MD5SUM_x86_64="0c594fe666e0332db1df9d160d7fabc8" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" -- cgit v1.2.3