Commit ea99f88f authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Singularity file added

parent 2852dc14
examples-dev/
docs.old/
examples/dev/
examples/tmp/
docs/olds/
################################################################################
# PYTHON #
......
Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
Wolfgang Rieping, and Michael Nilges
All rights reserved.
NO WARRANTY. This software package is provided 'as is' without warranty of
any kind, expressed or implied, including, but not limited to the implied
warranties of merchantability and fitness for a particular purpose or
a warranty of non-infringement.
Distribution of substantively modified versions of this module is
prohibited without the explicit permission of the copyright holders.
\ No newline at end of file
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Bootstrap: docker
FROM: centos:centos7
%labels
maintainer Fabrice Allain <fabrice.allain@pasteur.fr>
package.name ariaec
package.version 0.2.3
package.homepage https://gitlab.pasteur.fr/bis-aria/ariaec
%post
####################################
# Installing system #
####################################
yum install -y epel-release
yum install -y tkinter
yum install -y python2-pip python-devel gcc make git wget
pip install --upgrade pip ; pip install --upgrade setuptools; pip install sphinx; pip install numpy; pip install matplotlib
#################################
# installing ariaec #
#################################
cd /
ARIAEC_VERS="0.2.3"
wget -O ariaec-${ARIAEC_VERS}.tar.gz https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar.gz
mkdir ariaec-${ARIAEC_VERS} && tar xzf ariaec-${ARIAEC_VERS}.tar.gz -C ariaec-${ARIAEC_VERS} --strip-components 1
cd ariaec-${ARIAEC_VERS}
python setup.py sdist
pip install dist/ariaec-*.tar.gz
#git clone https://gitlab.pasteur.fr/bis-aria/ariaec.git
#cd ariaec
pip install .
#################################
# cleaning image #
#################################
cd /
rm ariaec-${ARIAEC_VERS}.tar.gz
rm -Rf ariaec-${ARIAEC_VERS}
yum remove --setopt=clean_requirements_on_remove=1 -y make git gcc wget
%runscript
CMD="$1"
shift
ARGS=${@}
case ${CMD} in
maptools )
exec /usr/bin/ariaec ${ARGS} ;;
main )
exec /usr/bin/aria2 ${ARGS} ;;
* )
echo "command \"${CMD}\" is not supported. available commands: \"coverage\"|\"htmp\""
exit 127
;;
esac
ariaec "$@"
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......@@ -19,6 +19,7 @@ from conkit.core.sequencefile import SequenceFile
from .common import sort_2dict
from .protmap import (ResMap, ResAtmMap)
LOG = logging.getLogger(__name__)
# TODO: check if Atom is still used ...
# TODO: Should use conkit in the future
......
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = AriaEc
SOURCEDIR = .
BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: cbf8f1a8c4c0d68994ae9bd4f214590d
tags: 645f666f9bcd5a90fca523b33c5a78b7
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