SPM12: only Matlab 2017a is supported, but repo website only hosts 2018a

[jona-sassenhagen]

When installing SPM, http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/ does not host a precompiled R2017a SPM at the moment. However, neurodocker complains it only supports R2017a. See below for a MWE:

docker run --rm kaczmarj/neurodocker:v0.3.2 generate -b neurodebian -p apt --spm version=12 matlab_version=R2018a
Traceback (most recent call last):
  File "/usr/bin/neurodocker", line 11, in <module>
    load_entry_point('neurodocker', 'console_scripts', 'neurodocker')()
  File "/opt/neurodocker/neurodocker/neurodocker.py", line 281, in main
    subparser_functions[namespace.subparser_name](namespace)
  File "/opt/neurodocker/neurodocker/neurodocker.py", line 228, in generate
    df = Dockerfile(specs)
  File "/opt/neurodocker/neurodocker/generate.py", line 457, in __init__
    self.cmd = self._create_cmd()
  File "/opt/neurodocker/neurodocker/generate.py", line 478, in _create_cmd
    chunks = _get_dockerfile_chunks(self.specs)
  File "/opt/neurodocker/neurodocker/generate.py", line 436, in _get_dockerfile_chunks
    chunk = _get_dockerfile_chunk(instruction, options, specs)
  File "/opt/neurodocker/neurodocker/generate.py", line 414, in _get_dockerfile_chunk
    chunk = callable_(**options).cmd
  File "/opt/neurodocker/neurodocker/interfaces/spm.py", line 62, in __init__
    raise ValueError("Only MATLAB R2017a is supported (for now).")
ValueError: Only MATLAB R2017a is supported (for now).

[kaczmarj]

Hi @jona-sassenhagen - thanks for the report. I am aware of this issue and am fixing it in #143. The Matlab version that the SPM version is compiled for will be downloaded.

[jona-sassenhagen]

Thanks! Shall I close?

[kaczmarj]

Nope, let's wait until the fix is merged.

[jona-sassenhagen]

Closed by #2498 ?

[kaczmarj]

@jona-sassenhagen - unfortunately not. that PR is a workaround for this bug. i apologize, i haven't had time to work on this yet.

[jona-sassenhagen]

Np probs!

[kaczmarj]

@jona-sassenhagen - this should be fixed by #159.

to clarify syntax, you can generate spm12 dev dockerfile with

neurodocker generate docker --base=debian:stretch --pkg-manager=apt --spm12 version=dev

and singularity recipe with

neurodocker generate singularity --base=debian:stretch --pkg-manager=apt --spm12 version=dev

this will install matlab compiler runtime 2018a along with spm12 dev.

[jona-sassenhagen]

Thanks, but sadly I get a different issue now ...

jona@kai:~$ neurodocker generate singularity --base=debian:stretch --pkg-manager=apt --spm12 version=dev

Traceback (most recent call last):
  File "/home/jona/tools/miniconda3/bin/neurodocker", line 11, in <module>
    load_entry_point('neurodocker==0.4.0rc0', 'console_scripts', 'neurodocker')()
  File "/home/jona/tools/miniconda3/lib/python3.6/site-packages/neurodocker/neurodocker.py", line 349, in main
    subparser_functions[namespace.subsubparser_name](namespace)
  File "/home/jona/tools/miniconda3/lib/python3.6/site-packages/neurodocker/neurodocker.py", line 302, in generate
    print(recipe_obj.render())
  File "/home/jona/tools/miniconda3/lib/python3.6/site-packages/neurodocker/generators/singularity.py", line 109, in render
    self._fill_parts()
  File "/home/jona/tools/miniconda3/lib/python3.6/site-packages/neurodocker/generators/singularity.py", line 157, in _fill_parts
    interface = impl(pkg_manager=pkg_man, **params)
  File "/home/jona/tools/miniconda3/lib/python3.6/site-packages/neurodocker/interfaces/interfaces.py", line 14, in __init__
    super().__init__(self._name, *args, **kwargs)
  File "/home/jona/tools/miniconda3/lib/python3.6/site-packages/neurodocker/interfaces/_base.py", line 188, in __init__
    "No YAML entry for package '{}'".format(self._name)
ValueError: No YAML entry for package '_header'

This is on a fresh Ubuntu 18.04 with miniconda3. Any ideas?

[kaczmarj]

did you pip install neurodocker? it could be that pip does not install the required YAML files (which include the installation templates). i'll try in a fresh miniconda environment.

it's my first time packaging with pip :)

[jona-sassenhagen]

did you pip install neurodocker?

I think I am using master. Errrr. I should try with 0.4.0rc0 right?

[kaczmarj]

@jona-sassenhagen - the problem is on neurodocker's end. yaml files are not included when pip installing by default. i'm updating the setup.py file to fix that now.

[jona-sassenhagen]

Great.

[kaczmarj]

@jona-sassenhagen - this is fixed now.

can you pip install -U neurodocker? the yaml files should be included now. feel free to open a new issue if you run into problems.