diff --git a/academic/sim/README b/academic/sim/README new file mode 100644 index 0000000000..b8dec9d5ba --- /dev/null +++ b/academic/sim/README @@ -0,0 +1,9 @@ +SIM - Local similarity program + +SIM finds k best non-intersecting alignments between two sequences or +within a sequence using dynamic programming techniques. The alignments +are reported in order of decreasing similarity score and share no +aligned pairs. + +Once the alignment is computed, you can view it using "lalnview", a +graphical viewer program for pairwise alignments, available at SBo. diff --git a/academic/sim/References b/academic/sim/References new file mode 100644 index 0000000000..6e829c7445 --- /dev/null +++ b/academic/sim/References @@ -0,0 +1,3 @@ +Xiaoquin Huang and Webb Miller: +"A Time-Efficient, Linear-Space Local Similarity Algorithm" +Advances in Applied Mathematics, vol. 12 (1991), pp. 337-357. diff --git a/academic/sim/sim.SlackBuild b/academic/sim/sim.SlackBuild new file mode 100644 index 0000000000..6fb9c1b34e --- /dev/null +++ b/academic/sim/sim.SlackBuild @@ -0,0 +1,91 @@ +#!/bin/bash + +# Slackware build script for sim + +# Copyright 2023 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. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=sim +VERSION=${VERSION:-204} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +cp $CWD/${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 {} \; + +cc $SLKCFLAGS -o $PRGNAM ${PRGNAM}${VERSION}.c -lm +install -D -m 755 $PRGNAM $PKG/usr/bin/$PRGNAM + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a $PRGNAM.doc $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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 diff --git a/academic/sim/sim.info b/academic/sim/sim.info new file mode 100644 index 0000000000..c1026b3e92 --- /dev/null +++ b/academic/sim/sim.info @@ -0,0 +1,12 @@ +PRGNAM="sim" +VERSION="204" +HOMEPAGE="https://web.expasy.org/sim/" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sim/sim204.c \ +ftp://pbil.univ-lyon1.fr/pub/logiciel/lalnview/sim/sim.doc" +MD5SUM="69edf7f5aa1c58bb3ad37ad761a289c2 \ +70f4bf9be3b16369dc21467d15cc7b48" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/sim/slack-desc b/academic/sim/slack-desc new file mode 100644 index 0000000000..c38253a06f --- /dev/null +++ b/academic/sim/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------------------------------------------------------| +sim: sim (Local similarity program) +sim: +sim: SIM finds k best non-intersecting alignments between two sequences +sim: or within a sequence using dynamic programming techniques. The +sim: alignments are reported in order of decreasing similarity score and +sim: share no aligned pairs. Once the alignment is computed, you can view +sim: it using "lalnview" +sim: +sim: +sim: +sim: