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Diffstat (limited to 'academic')
-rw-r--r-- | academic/locarna/README | 48 | ||||
-rw-r--r-- | academic/locarna/locarna.SlackBuild | 107 | ||||
-rw-r--r-- | academic/locarna/locarna.info | 10 | ||||
-rw-r--r-- | academic/locarna/slack-desc | 19 |
4 files changed, 184 insertions, 0 deletions
diff --git a/academic/locarna/README b/academic/locarna/README new file mode 100644 index 000000000000..ff32b839d912 --- /dev/null +++ b/academic/locarna/README @@ -0,0 +1,48 @@ +LocARNA: Alignment of RNAs +========================== + +LocARNA is a collection of alignment tools for the structural analysis +of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns +and predicts common structures for your RNAs. In this way, LocARNA +performs Sankoff-like alignment and is in particular suited for +analyzing sets of related RNAs without known common structure. + +LocARNA distinguishes itself from many other Sankoff-style multiple +alignment programs by its performance and low memory complexity, high +accuracy, and richness of features. As unique features, it offers +structure-local alignment, flexible structure and anchor constraints, +and provides efficient computation of reliabilities in +sequence-structure alignment. The package offers a robust core of +features and is used as experimental platform for the incorporation of +new features in RNA sequence-structure alignment. + + +At its core, the package offers global and local multiple alignment of +RNAs. + +Multiple alignment can be performed in one of several different ways: + +* progressive alignment using sequence-structure alignment of profiles + +* progressive alignment after consistency transformation using +T-Coffee + +* progressive alignment using probabilistic consistency transformation + and sequence-structure profile alignments, optionally followed by + iterative refinement. + + +Besides of global alignment, LocARNA supports two kinds of +locality. Local alignment as it is known from sequence alignment, +identifies and aligns the best matching subsequences. This form of +locality is called sequence local to distinguish it from structural +locality. When performing structure local alignment, LocARNA +identifies and aligns the best matching substructures in the RNAs. The +sequences of those substructures can be discontinuous on the sequence +level, but remain connected via structural bonds. + +Alignment Reliabilities (LocARNA-P). In this special, probabilistic +mode of operation LocARNA supports the efficient computation of match +probabilities, probabilistic consistency transformation for more +accurate multiple alignment, and generates reliability profiles of +multiple alignments. diff --git a/academic/locarna/locarna.SlackBuild b/academic/locarna/locarna.SlackBuild new file mode 100644 index 000000000000..488e2cfec22b --- /dev/null +++ b/academic/locarna/locarna.SlackBuild @@ -0,0 +1,107 @@ +#!/bin/sh + +# Slackware build script for locarna + +# Copyright 2019 Rob van Nues <sborg63@disroot.org> +# 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=locarna +VERSION=${VERSION:-1.9.2.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +#from https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=locarna + +install -d $PKG/usr/lib${LIBDIRSUFFIX}/perl5 +# seems to be 'private': https://github.com/s-will/LocARNA/issues/34 +mv $PKG/usr/lib/perl $PKG/usr/lib${LIBDIRSUFFIX}/perl5/vendor_perl + +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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS README INSTALL COPYING ChangeLog \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +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/locarna/locarna.info b/academic/locarna/locarna.info new file mode 100644 index 000000000000..3614b6a9f247 --- /dev/null +++ b/academic/locarna/locarna.info @@ -0,0 +1,10 @@ +PRGNAM="locarna" +VERSION="1.9.2.2" +HOMEPAGE="http://www.bioinf.uni-freiburg.de/Software/LocARNA/" +DOWNLOAD="https://github.com/s-will/LocARNA/releases/download/v1.9.2.2/locarna-1.9.2.2.tar.gz" +MD5SUM="24901cf57d3ef4a615f1f7b886d08eb3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="ViennaRNA" +MAINTAINER="Rob van Nues" +EMAIL="sborg63@disroot.org" diff --git a/academic/locarna/slack-desc b/academic/locarna/slack-desc new file mode 100644 index 000000000000..b913a794a625 --- /dev/null +++ b/academic/locarna/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------------------------------------------------------| +locarna: locarna (Local RNA alignment on structural basis) +locarna: +locarna: LocARNA is a collection of alignment tools for the structural +locarna: analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously +locarna: aligns and predicts common structures for your RNAs. In this way, +locarna: LocARNA performs Sankoff-like alignment and is in particular suited +locarna: for analyzing sets of related RNAs without known common structure. +locarna: +locarna: Home:https://www.bioinf.uni-freiburg.de/Software/LocARNA/ +locarna: +locarna: |