def test__add_to_entrypoint():
cmd = "export FOO=bar"
truth = "sed -i '$i{}' $ND_ENTRYPOINT".format(cmd)
out = DF._add_to_entrypoint(cmd, with_run=False)
assert truth in out and "RUN" not in out
out = DF._add_to_entrypoint(cmd, with_run=True)
assert truth in out and "RUN" in out
def install_binaries(self):
"""Return command to download and install FreeSurfer binaries."""
from neurodocker.generate import _add_to_entrypoint
url = self._get_binaries_url()
if self.check_urls and self.version == 'dev':
raise ValueError(
"check_urls=True and version='dev' cannot be used "
"together. Set check_urls to False.")
elif self.check_urls:
check_url(url)
if self.exclude:
excluded_dirs = _get_dirs_to_exclude(self.exclude)
else:
excluded_dirs = ''
cmd = self._install_binaries_deps()
ent = _add_to_entrypoint("source $FREESURFER_HOME/SetUpFreeSurfer.sh",
with_run=False)
cmd += ('\n&& echo "Downloading FreeSurfer ..."'
"\n&& curl -sSL --retry 5 {url}"
"\n| tar xz -C /opt\n{excluded}"
"\n&& {entrypoint_cmd}"
"".format(url=url, excluded=excluded_dirs, entrypoint_cmd=ent))
cmd = indent("RUN", cmd)
env_cmd = "ENV FREESURFER_HOME=/opt/freesurfer"
return "\n".join((cmd, env_cmd))
def install_spm(self):
"""Return Dockerfile instructions to install standalone SPM."""
from neurodocker.generate import _add_to_entrypoint
url = self._get_spm_url()
mcr_path = posixpath.join(SPM.MCR_DEST,
SPM.MCR_VERSIONS[str(self.matlab_version)],
'')
spm_cmd = '/opt/spm{0}/run_spm{0}.sh {1}'.format(
self.version, mcr_path)
spmmcrcmd = 'export SPMMCRCMD="{} script"'.format(spm_cmd)
entrypoint_cmd = _add_to_entrypoint(spmmcrcmd, with_run=False)
comment = "# Install standalone SPM"
cmd = ('echo "Downloading standalone SPM ..."'
"\n&& curl -sSL --retry 5 -o spm.zip {url}"
"\n&& unzip -q spm.zip -d /opt"
"\n&& chmod -R 777 /opt/spm*"
"\n&& rm -rf spm.zip"
"\n&& {spm_cmd} quit"
"\n&& {entrypoint_cmd}"
"".format(url=url,
spm_cmd=spm_cmd,
entrypoint_cmd=entrypoint_cmd))
cmd = indent("RUN", cmd)
env_cmd = self._get_spm_env_cmd(mcr_path, spm_cmd)
return '\n'.join((comment, cmd, env_cmd))
def install_binaries(self, url):
"""Return Dockerfile instructions to install FSL using binaries hosted
on FSL's website.
"""
from neurodocker.generate import _add_to_entrypoint
cmd = self._install_binaries_deps()
cmd += ('\n&& echo "Downloading FSL ..."'
'\n&& curl -sSL --retry 5 {}'
'\n| tar zx -C /opt'.format(url))
if self.version >= LooseVersion('5.0.10'):
fsl_python = "/opt/fsl/etc/fslconf/fslpython_install.sh"
cmd += "\n&& /bin/bash {} -q -f /opt/fsl".format(fsl_python)
if self.eddy_5011:
cmd += self._install_eddy_5011()
ent_cmds = ["echo Some packages in this Docker container are non-free",
("echo If you are considering commercial use of this"
" container, please consult the relevant license:"),
"echo https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence",
"source $FSLDIR/etc/fslconf/fsl.sh"]
cmd += "\n&& {}".format(_add_to_entrypoint(ent_cmds, with_run=False))
cmd = indent("RUN", cmd)
env_cmd = ("FSLDIR=/opt/fsl"
"\nPATH=/opt/fsl/bin:$PATH")
env_cmd = indent("ENV", env_cmd)
return "\n".join((cmd, env_cmd))
def install_binaries(self):
"""Return command to download and install FreeSurfer binaries."""
from neurodocker.generate import _add_to_entrypoint
url = self._get_binaries_url()
if self.check_urls and self.version == 'dev':
raise ValueError(
"check_urls=True and version='dev' cannot be used "
"together. Set check_urls to False.")
elif self.check_urls:
check_url(url)
# https://github.com/nipy/workshops/blob/master/170327-nipype/docker/Dockerfile.complete#L8-L20
# TODO: allow users to choose which directories to exclude.
excluded_dirs = ("--exclude='freesurfer/trctrain'"
"\n--exclude='freesurfer/subjects/fsaverage_sym'"
"\n--exclude='freesurfer/subjects/fsaverage3'"
"\n--exclude='freesurfer/subjects/fsaverage4'"
"\n--exclude='freesurfer/subjects/fsaverage5'"
"\n--exclude='freesurfer/subjects/fsaverage6'"
"\n--exclude='freesurfer/subjects/cvs_avg35'"
"\n--exclude='freesurfer/subjects/cvs_avg35_inMNI152'"
"\n--exclude='freesurfer/subjects/bert'"
"\n--exclude='freesurfer/subjects/V1_average'"
"\n--exclude='freesurfer/average/mult-comp-cor'"
"\n--exclude='freesurfer/lib/cuda'"
"\n--exclude='freesurfer/lib/qt'")
cmd = self._install_binaries_deps()
ent = _add_to_entrypoint("source $FREESURFER_HOME/SetUpFreeSurfer.sh",
with_run=False)
cmd += ('\n&& echo "Downloading FreeSurfer ..."'
"\n&& curl -sSL --retry 5 {url}"
"\n| tar xz -C /opt\n{excluded}"
"\n&& {entrypoint_cmd}"
"".format(url=url, excluded=excluded_dirs, entrypoint_cmd=ent))
cmd = indent("RUN", cmd)
env_cmd = "ENV FREESURFER_HOME=/opt/freesurfer"
return "\n".join((cmd, env_cmd))
def add_min_recon_all(self):
"""Return Dockerfile instructions to install minimized version of
recon-all.
See https://github.com/freesurfer/freesurfer/issues/70 for more
information.
"""
from neurodocker.generate import _add_to_entrypoint
cmd = self._install_binaries_deps()
url = ("https://dl.dropbox.com/s/nnzcfttc41qvt31/"
"recon-all-freesurfer6-3.min.tgz")
ent = _add_to_entrypoint("source $FREESURFER_HOME/SetUpFreeSurfer.sh",
with_run=False)
cmd += ('\n&& echo "Downloading minimized FreeSurfer ..."'
"\n&& curl -sSL {} | tar xz -C /opt"
"\n&& {entrypoint_cmd}"
"".format(url, entrypoint_cmd=ent))
cmd = indent("RUN", cmd)
env_cmd = "ENV FREESURFER_HOME=/opt/freesurfer"
return "\n".join((cmd, env_cmd))
def install_binaries(self):
"""Return Dockerfile instructions to download and install MINC
binaries.
"""
from neurodocker.generate import _add_to_entrypoint
minc_url = self._get_binaries_urls(self.version)
beast_url = self.BEAST_URL['1.1']
models_09a_url = self.MODELS_URL['09a']
models_09c_url = self.MODELS_URL['09c']
if self.check_urls:
check_url(minc_url)
check_url(beast_url)
check_url(models_09a_url)
check_url(models_09c_url)
cmd = self._install_binaries_deps()
ent = _add_to_entrypoint("source /opt/minc/minc-toolkit-config.sh",
with_run=False)
cmd += self._get_install_cmd(minc_url, beast_url, models_09a_url,
models_09c_url, ent)
cmd = indent("RUN", cmd)
return cmd
def _get_source_activate_cmd(self):
from neurodocker.generate import _add_to_entrypoint
cmd = "source activate {}".format(self.env_name)
return "\n&& " + _add_to_entrypoint(cmd, with_run=False)
