python/ruffus: Added (Computation Pipeline library).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Rob van Nues
Willy Sudiarto Raharjo
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Ruffus is a Computation Pipeline library for python. It is
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open-sourced, powerful and user-friendly, and widely used in science
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and bioinformatics. Ruffus is designed to allow scientific and other
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analyses to be automated with the minimum of fuss and the least effort.
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Please cite Ruffus as: Leo Goodstadt (2010): Ruffus: a lightweight
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Python library for computational pipelines. Bioinformatics 26(21):
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2778-2779
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Optional requirement: graphviz
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#!/bin/sh
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# Slackware build script for ruffus
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# Copyright 2017 Rob van Nues
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=ruffus
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VERSION=${VERSION:-20160417}
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COMMIT=${COMMIT:-f669a3f5b22bbd6b68cb0ff5efd590220e5ed665}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$COMMIT
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tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz
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cd $PRGNAM-$COMMIT
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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python setup.py install --root=$PKG
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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README.rst LICENSE.TXT CHANGES.TXT MANIFEST USAGE.TXT \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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PRGNAM="ruffus"
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VERSION="20160417"
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HOMEPAGE="http://www.ruffus.org.uk"
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DOWNLOAD="https://github.com/bunbun/ruffus/archive/f669a3f/ruffus-f669a3f5b22bbd6b68cb0ff5efd590220e5ed665.tar.gz"
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MD5SUM="45cf4b96159f0d85397a0fd4f58c75eb"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Rob van Nues"
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EMAIL="rvnues at tesco {dot} net"
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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ruffus: ruffus (Computation Pipeline library)
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ruffus:
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ruffus: Ruffus is a Computation Pipeline library for Python designed to allow
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ruffus: scientific and other analyses to be automated with the minimum of
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ruffus: fuss and the least effort.
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ruffus:
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ruffus: http://www.ruffus.org.uk
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ruffus:
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ruffus:
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ruffus:
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ruffus:
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