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Merge pull request #323 from cokelaer/dev
General cleanup before major release
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| New singularity images will be hosted on damona (damona.readthedocs.io) | ||
| The Singularity provided here was created for version 0.6.2 |
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| BootStrap: docker | ||
| From: ubuntu:latest | ||
| From: ubuntu:22.10 | ||
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| ############################################### | ||
| # do not change. This is a tagged version 0.4.3 | ||
| ############################################## | ||
| # do not change. This is a tagged version 0.6.1 | ||
| ############################################### | ||
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| %labels | ||
| maintainer Bertrand Neron <bneron@pasteur.fr> | ||
| maintainer Thomas Cokelaer | ||
| package.name bioconvert | ||
| package.version 0.4.3 | ||
| package.homepage https://pypi.python.org/pypi/bioconvert/0.4.3 | ||
| package.version 0.6.2 | ||
| package.homepage https://pypi.python.org/pypi/bioconvert/0.6.2 | ||
| package.source.url https://github.com/bioconvert/bioconvert | ||
| package.license GPLv3 | ||
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| %files | ||
| environment_0.6.2.yml | ||
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| %post | ||
| ######### install system ######### | ||
| export BIOCONVERT_VERSION="0.4.3" | ||
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| apt-get update -y | ||
| apt-get install -y wget bzip2 build-essential | ||
| apt-get install -y libgl1-mesa-glx | ||
| apt-get install -y build-essential | ||
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| # install anaconda | ||
| if [ ! -d /usr/local/anaconda ]; then | ||
| # wget https://repo.continuum.io/miniconda/Miniconda3-4.3.14-Linux-x86_64.sh\ | ||
| # for now, we use 4.2.12 to have python3.5 by default so no need to | ||
| # create a new env saving space in the process. The reason for using 3.5 | ||
| # is inherent to the packages used at the moment. | ||
| wget https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh\ | ||
| -O anaconda.sh && \ | ||
| bash anaconda.sh -b -p /usr/local/anaconda && \ | ||
| rm anaconda.sh | ||
| fi | ||
| export BIOCONVERT_VERSION="0.6.2" | ||
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| # set anaconda path | ||
| export PATH=${PATH}:/usr/local/anaconda/bin | ||
| conda update conda | ||
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| conda config --add channels r | ||
| conda config --add channels defaults | ||
| conda config --add channels conda-forge | ||
| conda config --add channels bioconda | ||
| apt-get update -y | ||
| apt-get install -y wget bzip2 build-essential | ||
| apt-get install -y libgl1-mesa-glx | ||
| apt-get install -y build-essential | ||
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| # The main packages for sequana: | ||
| conda install --file https://raw.githubusercontent.com/biokit/bioconvert/master/requirements.txt | ||
| conda install --file https://raw.githubusercontent.com/biokit/bioconvert/master/requirements_tools.txt | ||
| # linux only: | ||
| conda install mosdepth --yes | ||
| # install python3.9 | ||
| wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh \ | ||
| -O anaconda.sh && \ | ||
| bash anaconda.sh -b -p /usr/local/anaconda && \ | ||
| rm anaconda.sh | ||
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| # set anaconda path | ||
| export PATH=${PATH}:/usr/local/anaconda/bin | ||
| conda update conda | ||
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| #conda install -y graphviz==2.38 pygraphviz | ||
| # The main packages for bioconvert: | ||
| conda env update -f environment_0.6.2.yml --prune | ||
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| ######### install bioconvert ######### | ||
| pip install biocode | ||
| pip install bioconvert==${BIOCONVERT_VERSION} | ||
| ######### install bioconvert ######### | ||
| /usr/local/anaconda/envs/bioconvert/bin/pip3 install biocode | ||
| /usr/local/anaconda/envs/bioconvert/bin/pip3 install bioconvert==${BIOCONVERT_VERSION} | ||
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| if [ ! -d /etc/localtime ]; then | ||
| mkdir /etc/localtime | ||
| fi | ||
| # Uses agg as backend instead of qt (less dependencies) | ||
| echo "backend:tkagg" > matplotlibrc | ||
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| # Uses agg as backend instead of qt (less dependencies) | ||
| echo "backend:tkagg" > matplotlibrc | ||
| ######## clean image ######## | ||
| apt-get autoremove -y | ||
| apt-get clean -y | ||
| conda clean -y --all | ||
| rm -rf /usr/local/anaconda/pkgs | ||
| export PATH=${PATH}:/usr/local/anaconda/envs/bioconvert/bin | ||
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| ######## clean image ######## | ||
| apt-get autoremove -y | ||
| apt-get clean -y | ||
| conda clean -y --all | ||
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| %environment | ||
| export PATH=${PATH}:/usr/local/anaconda/bin | ||
| export PATH=${PATH}:/usr/local/anaconda/envs/bioconvert/bin | ||
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| %runscript | ||
| exec /usr/local/anaconda/bin/bioconvert "$@" | ||
| exec /usr/local/anaconda/envs/bioconvert/bin/bioconvert "$@" | ||
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