def test_build_image_fsl_509_binaries_stretch(self):
"""Install FSL binaries on Debian Stretch."""
specs = {'pkg_manager': 'apt',
'check_urls': True,
'instructions': [
('base', 'debian:stretch'),
('fsl', {'version': '5.0.9', 'use_binaries': True})
]}
container = utils.get_container_from_specs(specs)
output = container.exec_run('bash -c "bet"')
assert "error" not in output, "error running bet"
utils.test_cleanup(container)
def test_build_image_fsl_latest_pyinstaller_centos7(self):
"""Install latest FSL with FSL's Python installer on CentOS 7."""
specs = {'pkg_manager': 'yum',
'check_urls': True,
'instructions': [
('base', 'centos:7'),
('fsl', {'version': '5.0.10', 'use_binaries': True}),
('user', 'neuro'),
]}
container = utils.get_container_from_specs(specs)
output = container.exec_run('bash -c "bet"')
assert "error" not in output, "error running bet"
utils.test_cleanup(container)
def test_build_image_mrtrix3_binaries_centos7(self):
"""Install MRtrix3 binaries on CentOS 7."""
specs = {
'pkg_manager':
'yum',
'check_urls':
True,
'instructions': [
('base', 'centos:7'),
('mrtrix3', {
'use_binaries': True
}),
('user', 'neuro'),
]
}
container = utils.get_container_from_specs(specs)
output = container.exec_run('mrinfo')
assert "error" not in output, "error running mrinfo"
utils.test_cleanup(container)
def test_build_image_ants_210_binaries_centos7(self):
"""Install ANTs 2.1.0 binaries on CentOS 7."""
specs = {
'pkg_manager':
'yum',
'check_urls':
True,
'instructions': [
('base', 'centos:7'),
('ants', {
'version': '2.2.0',
'use_binaries': True
}),
('user', 'neuro'),
]
}
container = utils.get_container_from_specs(specs)
output = container.exec_run('Atropos')
assert "error" not in output, "error running Atropos"
utils.test_cleanup(container)
def test_build_image_freesurfer_600_min_binaries_xenial(self):
"""Install minimized FreeSurfer binaries on Ubuntu Xenial."""
specs = {
'pkg_manager':
'apt',
'check_urls':
True,
'instructions': [
('base', 'ubuntu:xenial'),
('freesurfer', {
'version': '6.0.0',
'use_binaries': True,
'min': True
}),
('user', 'neuro'),
]
}
container = utils.get_container_from_specs(specs)
output = container.exec_run('bash -c "recon-all"')
assert "error" not in output, "error running recon-all"
utils.test_cleanup(container)
def test_build_image_afni_latest_binaries_stretch(self):
"""Install latest AFNI binaries on Debian stretch."""
specs = {
'pkg_manager':
'apt',
'check_urls':
True,
'instructions': [
('base', 'debian:stretch'),
('afni', {
'version': 'latest',
'use_binaries': True
}),
('user', 'neuro'),
]
}
container = utils.get_container_from_specs(specs)
output = container.exec_run('3dSkullStrip')
assert "error" not in output, "error running 3dSkullStrip"
utils.test_cleanup(container)
def test_build_image_spm_12_standalone_stretch(self):
"""Install standalone SPM12 and MATLAB MCR R2017a."""
specs = {'pkg_manager': 'apt',
'check_urls': True,
'instructions': [
('base', 'debian:stretch'),
('spm', {'version': '12', 'matlab_version': 'R2017a'}),
('user', 'neuro'),
]}
container = utils.get_container_from_specs(specs)
cmd = ["/bin/bash", "-c", """echo 'fprintf("desired output")' > /tmp/test.m """]
container.exec_run(cmd)
# QUESTION: how can we run the entrypoint on a container in the
# background? The cmd below is a workaround because the entrypoint is
# not being run, so SPMMCRCMD is not set.
cmd = ["/bin/bash", "-c",
'source /neurodocker/startup.sh true && $SPMMCRCMD /tmp/test.m']
output = container.exec_run(cmd)
assert "error" not in output.lower(), "error running SPM command"
assert "desired output" in output, "expected output not found"
utils.test_cleanup(container)
def test_build_image_miniconda_latest_shellscript_centos7(self):
"""Install latest version of Miniconda via ContinuumIO's installer
script on CentOS 7.
"""
specs = {'pkg_manager': 'yum',
'check_urls': True,
'instructions': [
('base', 'centos:7'),
('user', 'neuro'),
('miniconda', {
'env_name': 'default',
'python_version': '3.5.1',
'conda_install': ['traits'],
'pip_install': ['https://github.com/nipy/nipype/archive/master.tar.gz']
}),
('user', 'neuro'),
]}
container = utils.get_container_from_specs(specs)
output = container.exec_run('python -V')
assert "3.5.1" in output, "incorrect Python version"
output = container.exec_run('python -c "import nipype"')
assert "ImportError" not in output, "nipype not installed"
utils.test_cleanup(container)
def test_build_image_neurodebian_dcm2niix_xenial(self):
"""Install latest version of Miniconda via ContinuumIO's installer
script on Ubuntu Xenial.
"""
specs = {
'pkg_manager':
'apt',
'check_urls':
False,
'instructions': [
('base', 'debian:stretch'),
('neurodebian', {
'os_codename': 'stretch',
'download_server': 'usa-nh',
'full': True,
'pkgs': ['dcm2niix']
}),
('user', 'neuro'),
]
}
container = utils.get_container_from_specs(specs)
output = container.exec_run('dcm2niix -h')
assert "usage: dcm2niix" in output, "dcm2niix not working"
utils.test_cleanup(container)