update public distribution
based on internal repository c9a2ac8 2019-01-03 16:04:57 +0100 tagged rev-master-2.0.0
This commit is contained in:
118
extras/singularity/singularity_python2
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118
extras/singularity/singularity_python2
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BootStrap: debootstrap
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OSVersion: bionic
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MirrorURL: http://ch.archive.ubuntu.com/ubuntu/
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%help
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a singularity container for PMSCO.
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git clone requires an ssh key for git.psi.ch.
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try agent forwarding (-A option to ssh).
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#%setup
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# executed on the host system outside of the container before %post
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#
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# this will be inside the container
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# touch ${SINGULARITY_ROOTFS}/tacos.txt
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# this will be on the host
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# touch avocados.txt
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#%files
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# files are copied before %post
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#
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# this copies to root
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# avocados.txt
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# this copies to /opt
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# avocados.txt /opt
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#
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# this does not work
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# ~/.ssh/known_hosts /etc/ssh/ssh_known_hosts
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# ~/.ssh/id_rsa /etc/ssh/id_rsa
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%labels
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Maintainer Matthias Muntwiler
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Maintainer_Email matthias.muntwiler@psi.ch
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Python_Version 2.7
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%environment
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export PATH="/usr/local/miniconda3/bin:$PATH"
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export PYTHON_VERSION=2.7
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export SINGULAR_BRANCH="singular"
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export LC_ALL=C
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%post
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export PYTHON_VERSION=2.7
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export LC_ALL=C
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sed -i 's/$/ universe/' /etc/apt/sources.list
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apt-get update
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apt-get -y install \
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binutils \
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build-essential \
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doxygen \
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doxypy \
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f2c \
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g++ \
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gcc \
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gfortran \
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git \
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graphviz \
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libblas-dev \
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liblapack-dev \
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libopenmpi-dev \
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make \
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nano \
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openmpi-bin \
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openmpi-common \
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sqlite3 \
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swig \
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wget
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apt-get clean
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
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bash ~/miniconda.sh -b -p /usr/local/miniconda3
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export PATH="/usr/local/miniconda3/bin:$PATH"
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conda create -q --yes -n pmsco python=${PYTHON_VERSION}
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. /usr/local/miniconda3/bin/activate pmsco
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conda install -q --yes -n pmsco \
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pip \
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numpy \
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scipy \
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ipython \
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mpi4py \
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matplotlib \
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nose \
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mock \
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future \
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statsmodels
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conda clean --all -y
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/usr/local/miniconda3/envs/pmsco/bin/pip install periodictable attrdict fasteners
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#%test
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# test the image after build
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%runscript
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# executes command from command line
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. /usr/local/miniconda3/bin/activate pmsco
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exec echo "$@"
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%apprun install
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. /usr/local/miniconda3/bin/activate pmsco
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cd ~
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git clone https://git.psi.ch/pearl/pmsco.git pmsco
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cd pmsco
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git checkout develop
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git checkout -b ${SINGULAR_BRANCH}
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make all
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nosetests
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%apprun python
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. /usr/local/miniconda3/bin/activate pmsco
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exec python "${@}"
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%apprun conda
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. /usr/local/miniconda3/bin/activate pmsco
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exec conda "${@}"
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117
extras/singularity/singularity_python3
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117
extras/singularity/singularity_python3
Normal file
@ -0,0 +1,117 @@
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BootStrap: debootstrap
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OSVersion: bionic
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MirrorURL: http://ch.archive.ubuntu.com/ubuntu/
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%help
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a singularity container for PMSCO.
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git clone requires an ssh key for git.psi.ch.
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try agent forwarding (-A option to ssh).
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#%setup
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# executed on the host system outside of the container before %post
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#
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# this will be inside the container
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# touch ${SINGULARITY_ROOTFS}/tacos.txt
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# this will be on the host
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# touch avocados.txt
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#%files
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# files are copied before %post
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#
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# this copies to root
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# avocados.txt
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# this copies to /opt
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# avocados.txt /opt
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#
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# this does not work
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# ~/.ssh/known_hosts /etc/ssh/ssh_known_hosts
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# ~/.ssh/id_rsa /etc/ssh/id_rsa
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%labels
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Maintainer Matthias Muntwiler
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Maintainer_Email matthias.muntwiler@psi.ch
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Python_Version 3
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%environment
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export PATH="/usr/local/miniconda3/bin:$PATH"
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export PYTHON_VERSION=3
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export SINGULAR_BRANCH="singular"
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export LC_ALL=C
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%post
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export PYTHON_VERSION=3
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export LC_ALL=C
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sed -i 's/$/ universe/' /etc/apt/sources.list
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apt-get update
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apt-get -y install \
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binutils \
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build-essential \
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doxygen \
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doxypy \
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f2c \
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g++ \
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gcc \
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gfortran \
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git \
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graphviz \
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libblas-dev \
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liblapack-dev \
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libopenmpi-dev \
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make \
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openmpi-bin \
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openmpi-common \
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sqlite3 \
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swig \
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wget
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apt-get clean
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
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bash ~/miniconda.sh -b -p /usr/local/miniconda3
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export PATH="/usr/local/miniconda3/bin:$PATH"
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conda create -q --yes -n pmsco python=${PYTHON_VERSION}
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. /usr/local/miniconda3/bin/activate pmsco
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conda install -q --yes -n pmsco \
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pip \
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numpy \
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scipy \
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ipython \
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mpi4py \
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matplotlib \
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nose \
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mock \
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future \
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statsmodels
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conda clean --all -y
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/usr/local/miniconda3/envs/pmsco/bin/pip install periodictable attrdict fasteners
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#%test
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# test the image after build
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%runscript
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# executes command from command line
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source /usr/local/miniconda3/bin/activate pmsco
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exec echo "$@"
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%apprun install
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source /usr/local/miniconda3/bin/activate pmsco
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cd ~
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git clone https://git.psi.ch/pearl/pmsco.git pmsco
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cd pmsco
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git checkout develop
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git checkout -b ${SINGULAR_BRANCH}
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make all
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nosetests
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%apprun python
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source /usr/local/miniconda3/bin/activate pmsco
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exec python "${@}"
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%apprun conda
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source /usr/local/miniconda3/bin/activate pmsco
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exec conda "${@}"
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76
extras/vagrant/Vagrantfile
vendored
Normal file
76
extras/vagrant/Vagrantfile
vendored
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@ -0,0 +1,76 @@
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# -*- mode: ruby -*-
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# vi: set ft=ruby :
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# All Vagrant configuration is done below. The "2" in Vagrant.configure
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# configures the configuration version (we support older styles for
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# backwards compatibility). Please don't change it unless you know what
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# you're doing.
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Vagrant.configure("2") do |config|
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# The most common configuration options are documented and commented below.
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# For a complete reference, please see the online documentation at
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# https://docs.vagrantup.com.
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# Every Vagrant development environment requires a box. You can search for
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# boxes at https://vagrantcloud.com/search.
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config.vm.box = "singularityware/singularity-2.4"
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config.vm.box_version = "2.4"
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# Disable automatic box update checking. If you disable this, then
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# boxes will only be checked for updates when the user runs
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# `vagrant box outdated`. This is not recommended.
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# config.vm.box_check_update = false
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# Create a forwarded port mapping which allows access to a specific port
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# within the machine from a port on the host machine. In the example below,
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# accessing "localhost:8080" will access port 80 on the guest machine.
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# NOTE: This will enable public access to the opened port
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# config.vm.network "forwarded_port", guest: 80, host: 8080
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# Create a forwarded port mapping which allows access to a specific port
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# within the machine from a port on the host machine and only allow access
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# via 127.0.0.1 to disable public access
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# config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
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# Create a private network, which allows host-only access to the machine
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# using a specific IP.
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# config.vm.network "private_network", ip: "192.168.33.10"
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# Create a public network, which generally matched to bridged network.
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# Bridged networks make the machine appear as another physical device on
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# your network.
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# config.vm.network "public_network"
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# Share an additional folder to the guest VM. The first argument is
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# the path on the host to the actual folder. The second argument is
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# the path on the guest to mount the folder. And the optional third
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# argument is a set of non-required options.
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# config.vm.synced_folder "../data", "/vagrant_data"
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# Provider-specific configuration so you can fine-tune various
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# backing providers for Vagrant. These expose provider-specific options.
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# Example for VirtualBox:
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#
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config.vm.provider "virtualbox" do |vb|
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# Display the VirtualBox GUI when booting the machine
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# vb.gui = true
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# Customize the amount of memory on the VM:
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# Increase this number if you plan to run parallel processes.
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vb.memory = "2048"
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# Customize the number of CPUs:
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# Increase as necessary but not more than physically available on the host.
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vb.cpus = 2
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end
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#
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# View the documentation for the provider you are using for more
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# information on available options.
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# Enable provisioning with a shell script. Additional provisioners such as
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# Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
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# documentation for more information about their specific syntax and use.
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# config.vm.provision "shell", inline: <<-SHELL
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# apt-get update
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# apt-get install -y apache2
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# SHELL
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end
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Reference in New Issue
Block a user