ReproNim/containers - containerized environments for reproducible neuroimaging

This repository provides a DataLad dataset (git/git-annex repository) with a collection of popular computational tools provided within ready to use containerized environments. At the moment it provides only Singularity images. Versions of all images are tracked using git-annex with content of the images provided from a dedicated Singularity Hub Collection or other original collections.

The main purpose is to be able to include this repository as a subdataset within larger study (super)datasets to facilitate rapid and reproducible computation, while

• adhering to YODA principles and retaining clear and unambiguous association between data, code, and computing environments using git/git-annex/DataLad;
• executing in "sanitized" containerized environments: no $HOME or system-wide /tmp is bind-mounted inside the containers, no environment variables from the host system made available inside.

All images are "registered" within the dataset for execution using datalad containers-run, so it is trivial to list available containers:

$> datalad containers-list
containers(ok): /home/yoh/proj/repronim/containers/images/bids/bids-validator--1.2.3.sing (file)
containers(ok): /home/yoh/proj/repronim/containers/images/bids/bids-freesurfer--6.0.1-5.sing (file)
containers(ok): /home/yoh/proj/repronim/containers/images/bids/bids-fmriprep--1.3.2.sing (file)
containers(ok): /home/yoh/proj/repronim/containers/images/bids/bids-magetbrain--0.3.sing (file)
...
containers(ok): /home/yoh/proj/repronim/containers/images/repronim/repronim-reproin--0.5.4.sing (file)
action summary:
  containers (ok: 21)

and execute either via datalad containers-run (which would also take care about getting them first if not present):

$> datalad containers-run -n bids-validator -- --help
[INFO   ] Making sure inputs are available (this may take some time)
[INFO   ] == Command start (output follows) ===== 
Usage: bids-validator <dataset_directory> [options]

Options:
  --help, -h            Show help                                      [boolean]
  --version, -v         Show version number                            [boolean]
  --ignoreWarnings      Disregard non-critical issues                  [boolean]
  --ignoreNiftiHeaders  Disregard NIfTI header content during validation
                                                                       [boolean]
  --verbose             Log more extensive information about issues    [boolean]
  --json                Output results as JSON                         [boolean]
  --config, -c          Optional configuration file. See
                        https://github.com/bids-standard/bids-validator for more
                        info

This tool checks if a dataset in a given directory is compatible with the Brain
Imaging Data Structure specification. To learn more about Brain Imaging Data
Structure visit http://bids.neuroimaging.io
[INFO   ] == Command exit (modification check follows) ===== 
action summary:
  get (notneeded: 1)
  save (notneeded: 1)

or first getting them using datalad get and then either using singularity run or exec directly, or (recommended) via scripts/singularity_cmd. That is the helper which is used by containers-run (see .datalad/config).

scripts/singularity_cmd

Singularity execution by default is optimized for convenience and not for reproducibility. This helper script assists in making singularity execution reproducible by

• disabling passing environment variables inside your containerized environment
• creating temporary /tmp directory for the environment, so there is no interaction with file paths outside of the current directory (which should ideally be a DataLad dataset)
• using custom and nearly empty binds/HOME HOME directory, so there is no possible leakage of locally user-level installed Python and other modules to affect your computation

The binds/HOME also provides a custom minimalistic .bashrc file with e.g. a customized prompt to inform you about which image you are in ATM for use in interactive sessions:

$> scripts/singularity_cmd exec images/repronim/repronim-reproin--0.5.4.sing bash
singularity:repronim-reproin--0.5.4 > yoh@hopa:/home/yoh/proj/repronim/containers$ heudiconv --version
0.5.4

See WiP PR #9 to establish "reproducible interactive sessions" with the help of that script.

Conventions

Container image files

Singularity image files have .sing extension. Since we are providing a custom filename to store the file at, we cannot guess the format of the container (e.g., either it is .sif), so we just use uniform .sing extension.

A typical workflow

Here is an outline of a simple analysis workflow, where we will adhere to [YODA] principles where each component should contain all necessary for its "reproduction" history and components

# Create fmriprep'ed dataset
datalad create -d data/raiders-fmriprep
cd data/raiders-fmriprep
# Install our containers collection:
datalad install -d . http://github.com/ReproNim/containers
# Populate with input data:
datalad install -d . -s ///labs/haxby/raiders sourcedata
# Execute desired preprocessing while creating a provenance record
# in git history
datalad containers-run \
	-n containers/bids-fmriprep \
	--input	sourcedata \
	--output . \
	{inputs} {outputs} participant

and now you have a dataset which has a git record on how these data was created, and could be redone later in time (by anyone) using datalad rerun. You can even now datalad uninstall sourcedata and even containers sub-datasets to save space - they will be retreavable at those exact versions later on if you need to extend or redo your analysis.

Note: aforementioned example requires DataLad >= 0.11.5 and datalad-containers >= 0.4.0

Installation

It is a DataLad dataset, so you can either just [git clone] or [datalad install] it. You will need to have [git annex] available to retrieve any images. And you will need DataLad and [datalad-container] extension installed for [datalad container-run]. Since Singularity is Linux-only application, it will be "functional" only on Linux. There is a WiP #3 to establish seamless execution of those Singularity images on systems which supports [Docker].

Environment variables

A few environment variables (in addition to those consulted by datalad and datalad-container) are considered in the scripts of this repository:

SINGULARITY_CMD

The default command (as "hardcoded" in [.datalad/config][]) is run so running the container executes its default "entry point". Setting SINGULARITY_CMD=exec makes it possible to run an alternative command in them (e.g. bash for interactive sessions)::

SINGULARITY_CMD=exec datalad containers-run --explicit -n repronim-reproin bash

and then have datalad record any of the introduced changes. Such runs will not be reproducible but at least clearly annotated in what environment corresponding actions were taken.