academic/mafft: Added (multiple sequence alignment program).

Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>

5 files changed, 207 insertions, 0 deletions

diff --git a/academic/mafft/README b/academic/mafft/README
new file mode 100644
index 0000000000000..bf887bcae624d
--- /dev/null
+++ b/academic/mafft/README
@@ -0,0 +1,8 @@
+MAFFT is a multiple sequence alignment program for unix-like operating
+systems.  It offers a range of multiple alignment methods, L-INS-i
+(accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for
+alignment of <∼10,000 sequences), etc.
+
+Visit the program website and check /usr/doc/mafft-* for citing and
+licensing informations: this program is released under a BSD license
+but its extensions use different ones.
diff --git a/academic/mafft/References b/academic/mafft/References
new file mode 100644
index 0000000000000..62541ce9e871a
--- /dev/null
+++ b/academic/mafft/References
@@ -0,0 +1,35 @@
+- Katoh, Frith 2012 (Bioinformatics Advance Access)
+  Adding unaligned sequences into an existing alignment using MAFFT
+  and LAST.
+  (describes the --add and --addfragments options)
+- Katoh, Toh 2010 (Bioinformatics 26:1899-1900)
+  Parallelization of the MAFFT multiple sequence alignment program.
+  (describes the multithread version)
+- Katoh, Asimenos, Toh 2009 (Methods in Molecular Biology 537:39-64)
+  Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics
+  for DNA Sequence Analysis edited by D. Posada
+  (outlines DNA alignment methods and several tips including
+  group-to-group alignment and rough clustering of a large
+  number of sequences)
+- Katoh, Toh 2008 (BMC Bioinformatics 9:212)
+  Improved accuracy of multiple ncRNA alignment by incorporating
+  structural information into a MAFFT-based framework.
+  (describes RNA structural alignment methods)
+- Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
+  Recent developments in the MAFFT multiple sequence alignment
+  program.
+  (outlines version 6; Fast Breaking Paper in Thomson Reuters'
+  ScienceWatch)
+- Katoh, Toh 2007 (Bioinformatics 23:372-374)  Errata
+  PartTree: an algorithm to build an approximate tree from a large
+  number of unaligned sequences.
+  (describes the PartTree algorithm)
+- Katoh, Kuma, Toh, Miyata 2005 (Nucleic Acids Res. 33:511-518)
+  MAFFT version 5: improvement in accuracy of multiple sequence
+  alignment.
+  (describes [ancestral versions of] the G-INS-i, L-INS-i and
+  E-INS-i strategies)
+- Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066)
+  MAFFT: a novel method for rapid multiple sequence alignment based
+  on fast Fourier transform.
+  (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) 
diff --git a/academic/mafft/mafft.SlackBuild b/academic/mafft/mafft.SlackBuild
new file mode 100644
index 0000000000000..9dee798f39772
--- /dev/null
+++ b/academic/mafft/mafft.SlackBuild
@@ -0,0 +1,135 @@
+#!/bin/sh
+
+# Slackware build script for mafft
+
+# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi
+# 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=mafft
+VERSION=${VERSION:-6.953}
+BUILD=${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-with-extensions
+tar xvf $CWD/$PRGNAM-$VERSION-with-extensions-src.tgz
+cd $PRGNAM-$VERSION-with-extensions
+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 core
+make clean
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+PREFIX=/usr \
+LIBDIR=/usr/libexec/$PRGNAM \
+MANDIR=/usr/man/man1 \
+make -e
+
+cd ../extensions
+make clean
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+PREFIX=/usr \
+LIBDIR=/usr/libexec/$PRGNAM \
+MANDIR=/usr/man/man1 \
+make -e
+
+cd ../core
+make \
+PREFIX=$PKG/usr \
+LIBDIR=$PKG/usr/libexec/$PRGNAM \
+MANDIR=$PKG/usr/man/man1 \
+install
+
+cd ../extensions
+make \
+PREFIX=$PKG/usr \
+LIBDIR=$PKG/usr/libexec/$PRGNAM \
+MANDIR=$PKG/usr/man/man1 \
+install
+
+cd ..
+
+# Clean up
+rm -rf $PKG/usr/libexec/$PRGNAM/{$PRGNAM.1,$PRGNAM-homologs.1}
+
+# Fix two wrong links
+( cd $PKG/usr/bin
+  rm -f mafft-distance mafft-profile
+  ln -s /usr/libexec/mafft/mafft-distance mafft-distance
+  ln -s /usr/libexec/mafft/mafft-profile mafft-profile )
+
+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 \
+  license license.extensions readme \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+# Fix permissions
+find $PKG/usr/doc -type f -exec chmod 0644 {} \;
+
+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.${PKGTYPE:-tgz}
diff --git a/academic/mafft/mafft.info b/academic/mafft/mafft.info
new file mode 100644
index 0000000000000..d72e1f0e901e0
--- /dev/null
+++ b/academic/mafft/mafft.info
@@ -0,0 +1,10 @@
+PRGNAM="mafft"
+VERSION="6.953"
+HOMEPAGE="http://mafft.cbrc.jp/alignment/software/"
+DOWNLOAD="http://mafft.cbrc.jp/alignment/software/mafft-6.953-with-extensions-src.tgz"
+MD5SUM="5ce2e3c5b97fb86aac90262191d61df3"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
diff --git a/academic/mafft/slack-desc b/academic/mafft/slack-desc
new file mode 100644
index 0000000000000..fff7b84f69049
--- /dev/null
+++ b/academic/mafft/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+     |-----handy-ruler------------------------------------------------------|
+mafft: mafft (A multiple sequence alignment program)
+mafft:
+mafft: MAFFT is a multiple sequence alignment program for unix-like
+mafft: operating systems.  It offers a range of multiple alignment
+mafft: methods, L-INS-i (accurate; for alignment of <∼200 sequences),
+mafft: FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
+mafft:
+mafft: Home: http://mafft.cbrc.jp/alignment/software/
+mafft: References: /usr/doc/mafft-$VERSION/References
+mafft:
+mafft: