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February 24, 2018 13:23
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Vagrantfile demo of cwltool+singularity+centos7
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# -*- mode: ruby -*- | |
# vi: set ft=ruby : | |
Vagrant.configure("2") do |config| | |
config.vm.box = "centos/7" | |
config.vm.provider "virtualbox" do |v| | |
v.linked_clone = true | |
end | |
config.vm.provision "shell", inline: <<-SHELL | |
sudo yum install -y gcc python-setuptools squashfs-tools git | |
curl --silent --location https://rpm.nodesource.com/setup_8.x | sudo bash - | |
sudo yum install -y nodejs | |
curl -O -L https://bootstrap.pypa.io/get-pip.py | |
sudo python get-pip.py | |
sudo pip install -U pip setuptools | |
sudo pip install cwltest | |
sudo pip install git+https://github.com/common-workflow-language/cwltool.git@singularity-support | |
curl -O -L https://github.com/singularityware/singularity/releases/download/2.4.2/singularity-2.4.2.tar.gz | |
tar xzf singularity-2.4.2.tar.gz | |
cd singularity-2.4.2 | |
./configure --prefix=/usr/local | |
make | |
sudo make install | |
hash -r | |
cd .. | |
curl -O -L https://github.com/common-workflow-language/common-workflow-language/archive/master.tar.gz | |
tar xzf master.tar.gz | |
cd common-workflow-language-master/ | |
PATH=$PATH:/usr/local/bin ./run_test.sh RUNNER=cwltool EXTRA=--singularity | |
SHELL | |
end |
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# -*- mode: ruby -*- | |
# vi: set ft=ruby : | |
Vagrant.configure("2") do |config| | |
# The most common configuration options are documented and commented below. | |
# For a complete reference, please see the online documentation at | |
# https://docs.vagrantup.com. | |
config.vm.box = "singularityware/singularity-2.4" | |
config.vm.box_version = "2.4" | |
config.vm.provider "virtualbox" do |v| | |
v.linked_clone = true | |
end | |
config.vm.provision "shell", inline: <<-SHELL | |
sudo apt-get install -y gcc python-setuptools squashfs-tools git nodejs | |
curl -O -L https://bootstrap.pypa.io/get-pip.py | |
sudo python get-pip.py | |
sudo pip install -U pip setuptools | |
sudo pip install cwltest | |
sudo pip install git+https://github.com/common-workflow-language/cwltool.git@singularity-support | |
curl -O -L https://github.com/common-workflow-language/common-workflow-language/archive/master.tar.gz | |
tar xzf master.tar.gz | |
cd common-workflow-language-master/ | |
PATH=$PATH:/usr/local/bin ./run_test.sh RUNNER=cwltool EXTRA=--singularity | |
SHELL | |
end |
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