diff options
| -rw-r--r-- | academic/muscle/README | 9 | ||||
| -rw-r--r-- | academic/muscle/References | 9 | ||||
| -rw-r--r-- | academic/muscle/muscle.SlackBuild | 76 | ||||
| -rw-r--r-- | academic/muscle/muscle.info | 10 | ||||
| -rw-r--r-- | academic/muscle/slack-desc | 19 |
5 files changed, 123 insertions, 0 deletions
diff --git a/academic/muscle/README b/academic/muscle/README new file mode 100644 index 000000000000..51ca74d7bfd1 --- /dev/null +++ b/academic/muscle/README @@ -0,0 +1,9 @@ +MUSCLE is a program for creating multiple alignments of amino acid or +nucleotide sequences. A range of options is provided that give you the +choice of optimizing accuracy, speed, or some compromise between the +two. + +For details and citation: +Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high +accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. +doi:10.1093/nar/gkh340
\ No newline at end of file diff --git a/academic/muscle/References b/academic/muscle/References new file mode 100644 index 000000000000..0615e580216e --- /dev/null +++ b/academic/muscle/References @@ -0,0 +1,9 @@ +References + +Edgar, R.C. (2004) MUSCLE: multiple sequence alignment +with high accuracy and high throughput. Nucleic Acids +Res. 32(5):1792-1797. doi:10.1093/nar/gkh340 + +Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method +with reduced time and space complexity BMC Bioinformatics, (5) +113. doi:10.1186/1471-2105-5-113 diff --git a/academic/muscle/muscle.SlackBuild b/academic/muscle/muscle.SlackBuild new file mode 100644 index 000000000000..10d32e72bfa1 --- /dev/null +++ b/academic/muscle/muscle.SlackBuild @@ -0,0 +1,76 @@ +#!/bin/sh + +# Slackware build script for muscle +# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and +# hereby submitted to the public domain + +# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING +# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ +# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. + +PRGNAM=muscle +VERSION=${VERSION:-3.8.31} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -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}_src.tar.gz +cd ${PRGNAM}${VERSION} +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +cd ./src + +ENV_GCC_OPTS="$SLKCFLAGS" \ + make + +install -D -m755 muscle $PKG/usr/bin/muscle + +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 +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.${PKGTYPE:-tgz} diff --git a/academic/muscle/muscle.info b/academic/muscle/muscle.info new file mode 100644 index 000000000000..956b8178c21a --- /dev/null +++ b/academic/muscle/muscle.info @@ -0,0 +1,10 @@ +PRGNAM="muscle" +VERSION="3.8.31" +HOMEPAGE="http://www.drive5.com/muscle/" +DOWNLOAD="http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz" +MD5SUM="f767f00fd15f0c5db944d41936779e10" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc new file mode 100644 index 000000000000..0a92681bd75e --- /dev/null +++ b/academic/muscle/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +muscle: muscle (A multiple sequence alignments program) +muscle: +muscle: MUSCLE is a program for creating multiple alignments of amino acid +muscle: or nucleotide sequences. A range of options is provided that give +muscle: you the choice of optimizing accuracy, speed, or some compromise +muscle: between the two. +muscle: +muscle: +muscle: +muscle: References: /usr/doc/muscle-$VERSION/References +muscle: Home: http://www.drive5.com/muscle/ |