diff options
Diffstat (limited to 'python/ruffus')
-rw-r--r-- | python/ruffus/README | 10 | ||||
-rw-r--r-- | python/ruffus/ruffus.SlackBuild | 88 | ||||
-rw-r--r-- | python/ruffus/ruffus.info | 10 | ||||
-rw-r--r-- | python/ruffus/slack-desc | 19 |
4 files changed, 127 insertions, 0 deletions
diff --git a/python/ruffus/README b/python/ruffus/README new file mode 100644 index 0000000000000..8086f4afd9c42 --- /dev/null +++ b/python/ruffus/README @@ -0,0 +1,10 @@ +Ruffus is a Computation Pipeline library for python. It is +open-sourced, powerful and user-friendly, and widely used in science +and bioinformatics. Ruffus is designed to allow scientific and other +analyses to be automated with the minimum of fuss and the least effort. + +Please cite Ruffus as: Leo Goodstadt (2010): Ruffus: a lightweight +Python library for computational pipelines. Bioinformatics 26(21): +2778-2779 + +Optional requirement: graphviz diff --git a/python/ruffus/ruffus.SlackBuild b/python/ruffus/ruffus.SlackBuild new file mode 100644 index 0000000000000..cb46a64ad35d5 --- /dev/null +++ b/python/ruffus/ruffus.SlackBuild @@ -0,0 +1,88 @@ +#!/bin/sh + +# Slackware build script for ruffus + +# Copyright 2017 Rob van Nues +# 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=ruffus +VERSION=${VERSION:-20160417} +COMMIT=${COMMIT:-f669a3f5b22bbd6b68cb0ff5efd590220e5ed665} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$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 $PRGNAM-$COMMIT +tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz +cd $PRGNAM-$COMMIT +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 {} \; + +python setup.py install --root=$PKG + +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 \ + README.rst LICENSE.TXT CHANGES.TXT MANIFEST USAGE.TXT \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +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/python/ruffus/ruffus.info b/python/ruffus/ruffus.info new file mode 100644 index 0000000000000..88b4431990b54 --- /dev/null +++ b/python/ruffus/ruffus.info @@ -0,0 +1,10 @@ +PRGNAM="ruffus" +VERSION="20160417" +HOMEPAGE="http://www.ruffus.org.uk" +DOWNLOAD="https://github.com/bunbun/ruffus/archive/f669a3f/ruffus-f669a3f5b22bbd6b68cb0ff5efd590220e5ed665.tar.gz" +MD5SUM="45cf4b96159f0d85397a0fd4f58c75eb" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Rob van Nues" +EMAIL="rvnues at tesco {dot} net" diff --git a/python/ruffus/slack-desc b/python/ruffus/slack-desc new file mode 100644 index 0000000000000..f6c237018be1e --- /dev/null +++ b/python/ruffus/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------------------------------------------------------| +ruffus: ruffus (Computation Pipeline library) +ruffus: +ruffus: Ruffus is a Computation Pipeline library for Python designed to allow +ruffus: scientific and other analyses to be automated with the minimum of +ruffus: fuss and the least effort. +ruffus: +ruffus: http://www.ruffus.org.uk +ruffus: +ruffus: +ruffus: +ruffus: |