From f8fb5e97dfa1dabbf7808f259e3bd9796f3e098c Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 9 Jun 2014 01:01:54 +0700 Subject: [PATCH] academic/geneconv: Added (Statistical Tests). Signed-off-by: Willy Sudiarto Raharjo --- academic/geneconv/README | 27 ++++++++ academic/geneconv/References | 29 ++++++++ academic/geneconv/geneconv.SlackBuild | 96 +++++++++++++++++++++++++++ academic/geneconv/geneconv.info | 14 ++++ academic/geneconv/slack-desc | 19 ++++++ 5 files changed, 185 insertions(+) create mode 100644 academic/geneconv/README create mode 100644 academic/geneconv/References create mode 100644 academic/geneconv/geneconv.SlackBuild create mode 100644 academic/geneconv/geneconv.info create mode 100644 academic/geneconv/slack-desc diff --git a/academic/geneconv/README b/academic/geneconv/README new file mode 100644 index 0000000000..885f156f08 --- /dev/null +++ b/academic/geneconv/README @@ -0,0 +1,27 @@ +GENECONV: Statistical Tests for Detecting Gene Conversion + +Gene conversion is any process that causes a segment of DNA to be +copied onto another segment of DNA, or else appears to act in this +way. The target segment can be on the same chromosome, on a different +chromosome, or in a different organism. Short-segment gene conversion +is an important force in evolution, and often takes place at a higher +frequency than does point mutation. + +Given an alignment of DNA or protein sequences, GENECONV finds the +most likely candidates for aligned gene conversion events between +pairs of sequences in the alignment. The program can also look for +gene conversion events from outside of the alignment. Candidate events +are ranked by multiple-comparison corrected P-values and listed to a +spreadsheet-like output file. + +IMPORTANT: +You may get a "Segmentation fault" when running the program; the +problem arises only when GENECONV writes to its log file (e.g. +myfile.nex.sum), as opposed to its main output file myfile.nex.frags; +the easiest workaround is to run GENECONV with the -nolog option: + +geneconv myfile.nex -nolog + +CITING: +For references and citation information, check the documentation +folder of the package. diff --git a/academic/geneconv/References b/academic/geneconv/References new file mode 100644 index 0000000000..5ca3d9f6c5 --- /dev/null +++ b/academic/geneconv/References @@ -0,0 +1,29 @@ +HOW TO CITE GENECONV (table of contents) + +A paper describing GENECONV has not yet appeared. In the meantime, try + +S. A. Sawyer (1999) GENECONV: A computer package for the statistical detection of gene conversion. Distributed by the author, Department of Mathematics, Washington University in St. Louis, available at http://www.math.wustl.edu/~sawyer. + +The reference + +Sawyer, S. A. (1989) Statistical tests for detecting gene conversion. Molecular Biology and Evolution 6, 526-538. + +is out of date for GENECONV, but could be used instead if journal policies only allow references to printed publications. + +Send email comments to [send email] sawyer@math.wustl.edu + +Maintained and supported by: + +Stanley Sawyer +Department of Mathematics +Washington University in St. Louis +St. Louis, Missouri 63130, USA + +Web address: http://www.math.wustl.edu/~sawyer +Email address: sawyer@math.wustl.edu + +This work was partially supported by NSF grant DMS-9707045. + +The program GENECONV is free for academic use, but commercial rights are reserved. +The program may be freely distributed for academic use, as long as it is not renamed or altered. +No warranty or guarantee of any kind is expressed or implied. diff --git a/academic/geneconv/geneconv.SlackBuild b/academic/geneconv/geneconv.SlackBuild new file mode 100644 index 0000000000..c87d532909 --- /dev/null +++ b/academic/geneconv/geneconv.SlackBuild @@ -0,0 +1,96 @@ +#!/bin/sh + +# Slackware build script for geneconv + +# Copyright 2014 Petar Petrov, petar.petrov@student.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=geneconv +VERSION=${VERSION:-1.81a} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=unix.source +DOCNAM=unix.examples + +if [ -z "$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" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +tar xvf $CWD/$SRCNAM.tar.gz +tar xvf $CWD/$DOCNAM.tar.gz +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# This is the program +cd $SRCNAM +gcc -DUNIX -o geneconv $SLKCFLAGS geneconv.c version.c vcalc.c vtcalc.c \ + vsetopts.c vread.c vdump.c vutil.c -lm + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM + +# These are the documentation examples +mkdir -p $PKG/usr/share/$PRGNAM +cp -a ../$DOCNAM/* $PKG/usr/share/$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 $CWD/gconvdoc.pdf $PKG/usr/doc/$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/geneconv/geneconv.info b/academic/geneconv/geneconv.info new file mode 100644 index 0000000000..00baacd720 --- /dev/null +++ b/academic/geneconv/geneconv.info @@ -0,0 +1,14 @@ +PRGNAM="geneconv" +VERSION="1.81a" +HOMEPAGE="http://www.math.wustl.edu/~sawyer/geneconv/" +DOWNLOAD="http://www.math.wustl.edu/~sawyer/geneconv/unix.source.tar.gz \ + http://www.math.wustl.edu/~sawyer/geneconv/unix.examples.tar.gz \ + http://www.math.wustl.edu/~sawyer/geneconv/gconvdoc.pdf" +MD5SUM="e558a7944261248314164dbfc256466b \ + 33ecd7178dc5c32de2e2ded37c9e6e05 \ + 399067c11bb638514be8d1ad741c4db9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/geneconv/slack-desc b/academic/geneconv/slack-desc new file mode 100644 index 0000000000..9c3ec97763 --- /dev/null +++ b/academic/geneconv/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------------------------------------------------------| +geneconv: geneconv (Statistical Tests for Detecting Gene Conversion) +geneconv: +geneconv: Given an alignment of DNA or protein sequences, GENECONV finds +geneconv: the most likely candidates for aligned gene conversion events +geneconv: between pairs of sequences in the alignment. The program can also +geneconv: look for gene conversion events from outside of the alignment. +geneconv: Candidate events are ranked by multiple-comparison corrected P- +geneconv: values and listed to a spreadsheet-like output file. +geneconv: +geneconv: Home: http://www.math.wustl.edu/~sawyer/geneconv/ +geneconv: References: /usr/doc/geneconv-1.81a/References