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DataLad

The DataLad Handbook at http://handbook.datalad.org is the ultimate introduction into DataLad.

An example of sample analysis using DataLad & containers

This is a WiP example on how to organize your study as DataLad dataset and use datalad-container extension to facilitate efficient and reproducible research:

# Create a dataset where we will keep all bits and pieces of a study
# With -c text2git we instruct to have data files to go to annex, while
# text files (code, docs, scripts) to git
datalad create -c text2git 1021_actions
cd 1021_actions
# Install a (sub)dataset with (Singularity) containers
datalad install -d . http://github.com/repronim/containers
# Install ReproIn'ed dataset from rolando
datalad install -d . -s rolando.cns.dartmouth.edu:/inbox/BIDS/Haxby/Sam/1021_actions bids
# Getting only a sample data (1 subject) for demonstration here
datalad get bids/sub-sid000005

TODO: finish

Meanwhile, have a look at

  • https://github.com/ReproNim/containers/#a-typical-workflow
  • a bit too convoluted ATM example with either datalad run or reproman run for scheduling parallel execution across cluster: https://github.com/ReproNim/reproman/pull/438
  • and possible future answers on https://neurostars.org/t/using-fmriprep-with-datalad-containers-run/5327