academic/bwa: Added (Burrows-Wheeler Aligner).

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

5 files changed, 149 insertions, 0 deletions

diff --git a/academic/bwa/README b/academic/bwa/README
new file mode 100644
index 0000000000000..fe07da7e2dfa6
--- /dev/null
+++ b/academic/bwa/README
@@ -0,0 +1,11 @@
+Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
+relatively short nucleotide sequences against a long reference
+sequence such as the human genome. It implements two algorithms, bwa-
+short and BWA-SW. The former works for query sequences shorter than
+200bp and the latter for longer sequences up to around 100kbp. Both
+algorithms do gapped alignment. They are usually more accurate and
+faster on queries with low error rates.
+
+If you use BWA-SW, please cite:
+Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
+Burrows-Wheeler Transform. Bioinformatics, Epub.
diff --git a/academic/bwa/References b/academic/bwa/References
new file mode 100644
index 0000000000000..e96223d8ecff6
--- /dev/null
+++ b/academic/bwa/References
@@ -0,0 +1,7 @@
+The short read alignment component (bwa-short) has been published:
+Li H. and Durbin R. (2009) Fast and accurate short read alignment
+with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.
+
+If you use BWA-SW, please cite:
+Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
+Burrows-Wheeler Transform. Bioinformatics, Epub.
diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild
new file mode 100644
index 0000000000000..32d7e7d6a9fc7
--- /dev/null
+++ b/academic/bwa/bwa.SlackBuild
@@ -0,0 +1,102 @@
+#!/bin/sh
+
+# Slackware build script for bwa
+
+# 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=bwa	
+VERSION=${VERSION:-0.6.2}
+BUILD=${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.bz2
+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 {} \;
+
+# Use our CFLAGS/CXXFLAGS
+sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
+
+# This is needed for the build on 32bit system
+sed -i "s:-DHAVE_PTHREAD #-D_NO_SSE2:-DHAVE_PTHREAD -D_NO_SSE2:" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+make
+
+install -D -m755 $PRGNAM	$PKG/usr/bin/$PRGNAM
+install -D -m644 $PRGNAM.1	$PKG/usr/man/man1/$PRGNAM.1
+ 
+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 \
+  ChangeLog COPYING 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
+
+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.${PKGTYPE:-tgz}
diff --git a/academic/bwa/bwa.info b/academic/bwa/bwa.info
new file mode 100644
index 0000000000000..0ef3c81947ca0
--- /dev/null
+++ b/academic/bwa/bwa.info
@@ -0,0 +1,10 @@
+PRGNAM="bwa"
+VERSION="0.6.2"
+HOMEPAGE="http://bio-bwa.sourceforge.net/"
+DOWNLOAD="http://downloads.sourceforge.net/bio-bwa/bwa-0.6.2.tar.bz2"
+MD5SUM="5e4043769ce3436f6098ec67f6e02332"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
diff --git a/academic/bwa/slack-desc b/academic/bwa/slack-desc
new file mode 100644
index 0000000000000..9d23eaa17cbd8
--- /dev/null
+++ b/academic/bwa/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+   |-----handy-ruler------------------------------------------------------|
+bwa: bwa (Burrows-Wheeler Aligner)
+bwa:
+bwa: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
+bwa: relatively short nucleotide sequences against a long reference
+bwa: sequence such as the human genome. It implements two algorithms,
+bwa: bwa-short and BWA-SW. The former works for query sequences shorter
+bwa: than 200bp and the latter for longer sequences up to around 100kbp.
+bwa:
+bwa: Home: http://bio-bwa.sourceforge.net/
+bwa: References: /usr/doc/bwa-$VERSION/References
+bwa: