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academic/RepeatMasker: Added (Screen DNA sequence).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
7e06cba42f
commit
08da4a154d
6 changed files with 180 additions and 0 deletions
31
academic/RepeatMasker/README
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31
academic/RepeatMasker/README
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RepeatMasker is a program that screens DNA sequences for interspersed
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repeats and low complexity DNA sequences. The output of the program is a
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detailed annotation of the repeats that are present in the query
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sequence as well as a modified version of the query sequence in which
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all the annotated repeats have been masked (default: replaced by Ns).
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Currently over 56% of human genomic sequence is identified and masked by
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the program. Sequence comparisons in RepeatMasker are performed by one
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of several popular search engines including:
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- nhmmer (part of 'HMMER', available on SBo)
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- Cross_Match. Due to licensing, you should obtain this yourself:
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http://www.phrap.org
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- ABBlast/WUBlast. Due to licensing, you should obtain this yourself:
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https://blast.advbiocomp.com/licensing/
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- RMBlast (found as 'ncbi-rmblastn' on SBo)
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RepeatMasker makes use of curated libraries of repeats and currently
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supports Dfam (profile HMM library derived from Repbase sequences) and
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Repbase, a service of the Genetic Information Research Institute.
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WARNING!
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Due to the bundled databases, the installed size of this is 1.8 GiB!
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NOTE!
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The package is installed in /opt. After install go fo /opt/RepeatMasker
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and run the RepeatMasker Configuration Program:
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# perl ./configure
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See README.SLACKWARE for details.
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31
academic/RepeatMasker/README.SLACKWARE
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31
academic/RepeatMasker/README.SLACKWARE
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After install go fo /opt/RepeatMasker and run the RepeatMasker
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Configuration Program:
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# perl ./configure
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Paths are as follows:
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**PERL PROGRAM**
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/usr/bin/perl
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**REPEATMASKER INSTALLATION DIRECTORY**
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/opt/RepeatMasker
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**TRF PROGRAM**
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/usr/bin/trf
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Add a Search Engine:
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1. CrossMatch: you should obtain this yourself, with the proper
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license, following the instructions here http://www.phrap.org/
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2. RMBlast - NCBI Blast with RepeatMasker extensions: this is
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available from SBo.
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3. WUBlast/ABBlast (required by DupMasker): you should obtain this
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yourself, with the proper license, following the instructions here
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https://blast.advbiocomp.com/licensing/
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4. HMMER3.1 & DFAM: this is available from SBo.
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**RMBlast (rmblastn) INSTALLATION PATH**
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/usr/bin
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**HMMER INSTALLATION PATH**
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/usr/bin
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9
academic/RepeatMasker/References
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9
academic/RepeatMasker/References
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Please use the following for both the website and the RepeatMasker software package:
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Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0.
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2013-2015 <http://www.repeatmasker.org>.
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or
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Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.
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1996-2010 <http://www.repeatmasker.org>.
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80
academic/RepeatMasker/RepeatMasker.SlackBuild
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80
academic/RepeatMasker/RepeatMasker.SlackBuild
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#!/bin/sh
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# Slackware build script for RepeatMasker
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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=RepeatMasker
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VERSION=${VERSION:-4.0.7}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCVER=${SRCVER:-4-0-7}
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ARCH=noarch
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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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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM
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tar xvf $CWD/$PRGNAM-open-$SRCVER.tar.gz
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cd $PRGNAM
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Place everything in /opt...
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mkdir -p $PKG/opt/$PRGNAM
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cp -a * $PKG/opt/$PRGNAM
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# Make a symlink
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mkdir -p $PKG/usr/bin
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cd $PKG/usr/bin
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ln -s ../../opt/$PRGNAM/$PRGNAM
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cd -
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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# Better just copy these and not move them from their original dir
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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daterepeats.help INSTALL license.txt README repeatmasker.help \
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$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/README.SLACKWARE > $PKG/usr/doc/$PRGNAM-$VERSION/README.SLACKWARE
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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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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10
academic/RepeatMasker/RepeatMasker.info
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10
academic/RepeatMasker/RepeatMasker.info
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PRGNAM="RepeatMasker"
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VERSION="4.0.7"
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HOMEPAGE="http://www.repeatmasker.org/"
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DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
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MD5SUM="4dcbd7c88c5343e02d819f4b3e6527c6"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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19
academic/RepeatMasker/slack-desc
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19
academic/RepeatMasker/slack-desc
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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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RepeatMasker: RepeatMasker (Screen DNA sequence for interspersed repeats)
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RepeatMasker:
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RepeatMasker: RepeatMasker is a program that screens DNA sequences for inter-
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RepeatMasker: spersed repeats and low complexity DNA sequences. The output of
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RepeatMasker: the program is a detailed annotation of the repeats that are
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RepeatMasker: present in the query sequence as well as a modified version of
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RepeatMasker: the query sequence in which all the annotated repeats have been
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RepeatMasker: masked (default: replaced by Ns).
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RepeatMasker:
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RepeatMasker: Home: http://www.repeatmasker.org/
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RepeatMasker:
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