diff options
Diffstat (limited to 'academic')
-rw-r--r-- | academic/RepeatMasker/README | 31 | ||||
-rw-r--r-- | academic/RepeatMasker/README.SLACKWARE | 31 | ||||
-rw-r--r-- | academic/RepeatMasker/References | 9 | ||||
-rw-r--r-- | academic/RepeatMasker/RepeatMasker.SlackBuild | 80 | ||||
-rw-r--r-- | academic/RepeatMasker/RepeatMasker.info | 10 | ||||
-rw-r--r-- | academic/RepeatMasker/slack-desc | 19 |
6 files changed, 180 insertions, 0 deletions
diff --git a/academic/RepeatMasker/README b/academic/RepeatMasker/README new file mode 100644 index 0000000000..a62062fa85 --- /dev/null +++ b/academic/RepeatMasker/README @@ -0,0 +1,31 @@ +RepeatMasker is a program that screens DNA sequences for interspersed +repeats and low complexity DNA sequences. The output of the program is a +detailed annotation of the repeats that are present in the query +sequence as well as a modified version of the query sequence in which +all the annotated repeats have been masked (default: replaced by Ns). + +Currently over 56% of human genomic sequence is identified and masked by +the program. Sequence comparisons in RepeatMasker are performed by one +of several popular search engines including: + +- nhmmer (part of 'HMMER', available on SBo) +- Cross_Match. Due to licensing, you should obtain this yourself: + http://www.phrap.org +- ABBlast/WUBlast. Due to licensing, you should obtain this yourself: + https://blast.advbiocomp.com/licensing/ +- RMBlast (found as 'ncbi-rmblastn' on SBo) + +RepeatMasker makes use of curated libraries of repeats and currently +supports Dfam (profile HMM library derived from Repbase sequences) and +Repbase, a service of the Genetic Information Research Institute. + +WARNING! +Due to the bundled databases, the installed size of this is 1.8 GiB! + +NOTE! +The package is installed in /opt. After install go fo /opt/RepeatMasker +and run the RepeatMasker Configuration Program: + +# perl ./configure + +See README.SLACKWARE for details. diff --git a/academic/RepeatMasker/README.SLACKWARE b/academic/RepeatMasker/README.SLACKWARE new file mode 100644 index 0000000000..dd3313fd62 --- /dev/null +++ b/academic/RepeatMasker/README.SLACKWARE @@ -0,0 +1,31 @@ +After install go fo /opt/RepeatMasker and run the RepeatMasker +Configuration Program: + +# perl ./configure + +Paths are as follows: + +**PERL PROGRAM** +/usr/bin/perl + +**REPEATMASKER INSTALLATION DIRECTORY** +/opt/RepeatMasker + +**TRF PROGRAM** +/usr/bin/trf + +Add a Search Engine: +1. CrossMatch: you should obtain this yourself, with the proper + license, following the instructions here http://www.phrap.org/ +2. RMBlast - NCBI Blast with RepeatMasker extensions: this is + available from SBo. +3. WUBlast/ABBlast (required by DupMasker): you should obtain this + yourself, with the proper license, following the instructions here + https://blast.advbiocomp.com/licensing/ +4. HMMER3.1 & DFAM: this is available from SBo. + +**RMBlast (rmblastn) INSTALLATION PATH** +/usr/bin + +**HMMER INSTALLATION PATH** +/usr/bin diff --git a/academic/RepeatMasker/References b/academic/RepeatMasker/References new file mode 100644 index 0000000000..e74438871f --- /dev/null +++ b/academic/RepeatMasker/References @@ -0,0 +1,9 @@ +Please use the following for both the website and the RepeatMasker software package: + +Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0. +2013-2015 <http://www.repeatmasker.org>. + +or + +Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0. +1996-2010 <http://www.repeatmasker.org>. diff --git a/academic/RepeatMasker/RepeatMasker.SlackBuild b/academic/RepeatMasker/RepeatMasker.SlackBuild new file mode 100644 index 0000000000..033e2ffbfd --- /dev/null +++ b/academic/RepeatMasker/RepeatMasker.SlackBuild @@ -0,0 +1,80 @@ +#!/bin/sh + +# Slackware build script for RepeatMasker + +# 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=RepeatMasker +VERSION=${VERSION:-4.0.7} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCVER=${SRCVER:-4-0-7} +ARCH=noarch + +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 +tar xvf $CWD/$PRGNAM-open-$SRCVER.tar.gz +cd $PRGNAM +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 {} \; + +# Place everything in /opt... +mkdir -p $PKG/opt/$PRGNAM +cp -a * $PKG/opt/$PRGNAM + +# Make a symlink +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/$PRGNAM/$PRGNAM +cd - + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +# Better just copy these and not move them from their original dir +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + daterepeats.help INSTALL license.txt README repeatmasker.help \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/README.SLACKWARE > $PKG/usr/doc/$PRGNAM-$VERSION/README.SLACKWARE +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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/RepeatMasker/RepeatMasker.info b/academic/RepeatMasker/RepeatMasker.info new file mode 100644 index 0000000000..751dfbd308 --- /dev/null +++ b/academic/RepeatMasker/RepeatMasker.info @@ -0,0 +1,10 @@ +PRGNAM="RepeatMasker" +VERSION="4.0.7" +HOMEPAGE="http://www.repeatmasker.org/" +DOWNLOAD="http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz" +MD5SUM="4dcbd7c88c5343e02d819f4b3e6527c6" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/RepeatMasker/slack-desc b/academic/RepeatMasker/slack-desc new file mode 100644 index 0000000000..2615519481 --- /dev/null +++ b/academic/RepeatMasker/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------------------------------------------------------| +RepeatMasker: RepeatMasker (Screen DNA sequence for interspersed repeats) +RepeatMasker: +RepeatMasker: RepeatMasker is a program that screens DNA sequences for inter- +RepeatMasker: spersed repeats and low complexity DNA sequences. The output of +RepeatMasker: the program is a detailed annotation of the repeats that are +RepeatMasker: present in the query sequence as well as a modified version of +RepeatMasker: the query sequence in which all the annotated repeats have been +RepeatMasker: masked (default: replaced by Ns). +RepeatMasker: +RepeatMasker: Home: http://www.repeatmasker.org/ +RepeatMasker: |