academic/clustalw: Added (Multiple Sequence Alignment)

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

5 files changed, 167 insertions, 0 deletions

diff --git a/academic/clustalw/README b/academic/clustalw/README
new file mode 100644
index 0000000000..a65458b66d
--- /dev/null
+++ b/academic/clustalw/README
@@ -0,0 +1,6 @@
+Clustal is a widely used, multiple sequence alignment program. This 
+is ClustalW, the command line tool. 
+
+For details and citation:
+Clustal W and Clustal X version 2.0, Larkin M., et al. Bioinformatics 
+2007 23(21):2947-2948
diff --git a/academic/clustalw/References b/academic/clustalw/References
new file mode 100644
index 0000000000..657db37a3b
--- /dev/null
+++ b/academic/clustalw/References
@@ -0,0 +1,38 @@
+References
+
+Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam
+H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ,
+Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics,
+23, 2947-2948.
+
+Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson
+JD. (2003). Multiple sequence alignment with the Clustal series of
+programs. Nucleic Acids Res., 31, 3497-3500.
+
+Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. (1998). Multiple
+sequence alignment with Clustal X. Trends Biochem Sci., 23, 403-405.
+
+Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The
+CLUSTAL_X windows interface: flexible strategies for multiple sequence
+alignment aided by quality analysis tools. Nucleic Acids Res., 25,
+4876-4882.
+
+Higgins DG, Thompson JD, Gibson TJ. (1996). Using CLUSTAL for multiple
+sequence alignments. Methods Enzymol., 266, 383-402.
+
+Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving
+the sensitivity of progressive multiple sequence alignment through
+sequence weighting, position-specific gap penalties and weight matrix
+choice. Nucleic Acids Res., 22, 4673-4680.
+
+Higgins DG. (1994). CLUSTAL V: multiple alignment of DNA and protein
+sequences. Methods Mol Biol., 25, 307-318
+
+Higgins DG, Bleasby AJ, Fuchs R. (1992). CLUSTAL V: improved software
+for multiple sequence alignment. Comput. Appl. Biosci., 8, 189-191.
+
+Higgins,DG and Sharp,PM (1989). Fast and sensitive multiple sequence
+alignments on a microcomputer. Comput. Appl. Biosci., 5, 151-153.
+
+Higgins,D.G. and Sharp,P.M. (1988). CLUSTAL: a package for performing
+multiple sequence alignment on a microcomputer. Gene, 73, 237-244.
diff --git a/academic/clustalw/clustalw.SlackBuild b/academic/clustalw/clustalw.SlackBuild
new file mode 100644
index 0000000000..bdef830583
--- /dev/null
+++ b/academic/clustalw/clustalw.SlackBuild
@@ -0,0 +1,94 @@
+#!/bin/sh
+
+# Slackware build script for clustalw
+# 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=clustalw			
+VERSION=${VERSION:-2.1}	
+BUILD=${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.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 {} \;
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+
+make
+make install DESTDIR=$PKG
+
+# Some programs expect the executable to be called clustalw, not clustalw2
+cd $PKG/usr/bin
+  ln -s clustalw2 clustalw
+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
+
+# This is empty 
+rm -rf $PKG/usr/share
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  COPYING COPYING.LESSER README clustalw_help \
+  $PKG/usr/doc/$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.${PKGTYPE:-tgz}
diff --git a/academic/clustalw/clustalw.info b/academic/clustalw/clustalw.info
new file mode 100644
index 0000000000..3fc948a033
--- /dev/null
+++ b/academic/clustalw/clustalw.info
@@ -0,0 +1,10 @@
+PRGNAM="clustalw"
+VERSION="2.1"
+HOMEPAGE="http://www.clustal.org/"
+DOWNLOAD="http://www.clustal.org/download/current/clustalw-2.1.tar.gz"
+MD5SUM="144df8440a0ae083d5167616c8ceeb41"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/clustalw/slack-desc b/academic/clustalw/slack-desc
new file mode 100644
index 0000000000..3afe2bcbde
--- /dev/null
+++ b/academic/clustalw/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.  Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in.  You must
+# make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':'.
+
+        |-----handy-ruler------------------------------------------------------|
+clustalw: clustalw (Multiple Sequence Alignment)
+clustalw:
+clustalw: CLUSTAL W: improving the sensitivity of progressive multiple sequence
+clustalw: alignment through sequence weighting, position-specific gap penalties
+clustalw: and weight matrix choice.
+clustalw:
+clustalw:
+clustalw:
+clustalw:
+clustalw: References: /usr/doc/clustalw-$VERSION/References
+clustalw: Home: http://www.clustal.org/