academic/muscle: Added (A multiple sequence alignments program)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

5 files changed, 123 insertions, 0 deletions

diff --git a/academic/muscle/README b/academic/muscle/README
new file mode 100644
index 0000000000..51ca74d7bf
--- /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 0000000000..0615e58021
--- /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 0000000000..10d32e72bf
--- /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.${PKGTYPE:-tgz}
diff --git a/academic/muscle/muscle.info b/academic/muscle/muscle.info
new file mode 100644
index 0000000000..956b8178c2
--- /dev/null
+++ b/academic/muscle/muscle.info
@@ -0,0 +1,10 @@
+PRGNAM="muscle"
+VERSION="3.8.31"
+HOMEPAGE="http://www.drive5.com/muscle/"
+DOWNLOAD="http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz"
+MD5SUM="f767f00fd15f0c5db944d41936779e10"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc
new file mode 100644
index 0000000000..0a92681bd7
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+++ b/academic/muscle/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.  Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in.  You must
+# make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':'.
+
+      |-----handy-ruler------------------------------------------------------|
+muscle: muscle (A multiple sequence alignments program)
+muscle:
+muscle: MUSCLE is a program for creating multiple alignments of amino acid
+muscle: or nucleotide sequences. A range of options is provided that give
+muscle: you the choice of optimizing accuracy, speed, or some compromise
+muscle: between the two.
+muscle:
+muscle:
+muscle:
+muscle: References: /usr/doc/muscle-$VERSION/References
+muscle: Home: http://www.drive5.com/muscle/