academic/Gblocks: Added (Select blocks of evolutionarily conserved sites)

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

5 files changed, 140 insertions, 0 deletions

diff --git a/academic/Gblocks/Gblocks.SlackBuild b/academic/Gblocks/Gblocks.SlackBuild
new file mode 100644
index 0000000000..fcb2a6006e
--- /dev/null
+++ b/academic/Gblocks/Gblocks.SlackBuild
@@ -0,0 +1,90 @@
+#!/bin/sh
+
+# Slackware build script for Gblocks
+
+# Copyright 2011  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=Gblocks			
+VERSION=${VERSION:-0.91b}	
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}		
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i386 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}	
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}	
+
+set -e
+
+if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
+  printf "\n\n$ARCH is not supported... \n"
+  exit 1
+fi
+
+# Determine the source arch
+if [ "$ARCH" = "x86_64" ]; then
+  SRCARCH="64"
+else
+  SRCARCH=""
+fi
+
+# Construct the tarball name
+TARNAME=${PRGNAM}_Linux${SRCARCH}_${VERSION}
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf ${PRGNAM}_${VERSION}
+tar xvf $CWD/$TARNAME.tar.Z
+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 {} \;
+
+install -D -m755 Gblocks $PKG/usr/bin/$PRGNAM
+
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a more_alignments/* $PKG/usr/share/$PRGNAM
+
+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
+cp -a Documentation/*  $PKG/usr/doc/$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/Gblocks/Gblocks.info b/academic/Gblocks/Gblocks.info
new file mode 100644
index 0000000000..0b50f869b1
--- /dev/null
+++ b/academic/Gblocks/Gblocks.info
@@ -0,0 +1,10 @@
+PRGNAM="Gblocks"
+VERSION="0.91b"
+HOMEPAGE="http://molevol.cmima.csic.es/castresana/Gblocks.html"
+DOWNLOAD="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux_0.91b.tar.Z"
+MD5SUM="8b62e8447eaea37a86c35e1bf5996580"
+DOWNLOAD_x86_64="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z"
+MD5SUM_x86_64="c2c752ae4cbfda0b8bf09e6662585252"
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="rworkman"
diff --git a/academic/Gblocks/README b/academic/Gblocks/README
new file mode 100644
index 0000000000..af80855a88
--- /dev/null
+++ b/academic/Gblocks/README
@@ -0,0 +1,14 @@
+Gblocks is a program written in ANSI C language that eliminates poorly
+aligned positions and divergent regions of an alignment of DNA or
+protein sequences. These positions may not be homologous or may have
+been saturated by multiple substitutions and it is convenient to
+eliminate them prior to phylogenetic analysis.
+
+The use of a program such as Gblocks reduces the necessity of manually
+editing multiple alignments, makes the automation of phylogenetic
+analysis of large data sets feasible and, finally, facilitates the
+reproduction of the alignments and subsequent phylogenetic analysis by
+other researchers. Gblocks is very fast in processing alignments and
+it is therefore highly suitable for large-scale phylogenetic analyses.
+
+This just repackages the binaries provided from upstream.
diff --git a/academic/Gblocks/References b/academic/Gblocks/References
new file mode 100644
index 0000000000..3c993b48d0
--- /dev/null
+++ b/academic/Gblocks/References
@@ -0,0 +1,7 @@
+Talavera, G., and Castresana, J. (2007). Improvement of phylogenies
+after removing divergent and ambiguously aligned blocks from protein
+sequence alignments. Systematic Biology 56, 564-577.
+
+Castresana, J. (2000). Selection of conserved blocks from multiple
+alignments for their use in phylogenetic analysis. Molecular Biology
+and Evolution 17, 540-552. 
\ No newline at end of file
diff --git a/academic/Gblocks/slack-desc b/academic/Gblocks/slack-desc
new file mode 100644
index 0000000000..99fbc635e6
--- /dev/null
+++ b/academic/Gblocks/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------------------------------------------------------|
+Gblocks: Gblocks (Select blocks of evolutionarily conserved sites)
+Gblocks:
+Gblocks: Gblocks is a program that eliminates poorly aligned positions and
+Gblocks: divergent regions of an alignment of DNA or protein sequences.
+Gblocks:
+Gblocks: References: /usr/doc/Gblocks-$VERSION/References
+Gblocks: Home: http://molevol.cmima.csic.es/castresana/Gblocks.html
+Gblocks:
+Gblocks:
+Gblocks:
+Gblocks: