BEst computational pipeline for CBRAIN

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Table of Contents

• BEst computational pipeline for CBRAIN
  • How the BEst container was built
    • 1. Compile BEst
      • Details
      • Main requirements
    • 2. Build the Docker container and push
      • Main requirements
    • 3. Build the Singularity container
    • 4. Test the image

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How the BEst container was built

1. Compile BEst

Using best_compile.bash:

~/programs/best-cbrain/for_build/best_compile.bash -d ~/wkdir/best-190729 -n best-app -c matlab18b

Details

~/programs/best-cbrain/for_build/best_compile.bash -h

Main requirements

• Linux OS
• MATLAB compiler

2. Build the Docker container and push

Using Dockerfile:

cp ~/programs/best-cbrain/for_build/containers/Dockerfile ~/wkdir/best-190729
docker build --no-cache -f ~/wkdir/best-190729/Dockerfile -t multifunkim/best:latest ~/wkdir/best-190729
docker push multifunkim/best:latest

Main requirements

• Compiled BEst archive
• BEst test dataset

3. Build the Singularity container

Choose one of these commands:

• Using Singularity:

sudo singularity build ~/programs/best-cbrain.simg ~/programs/best-cbrain/for_build/containers/Singularity

• From Docker Hub:

sudo singularity build ~/programs/best-cbrain.simg docker://multifunkim/best:latest

4. Test

singularity exec ~/programs/best-cbrain.simg /bin/bash -c 'BEst inputData $BEST_DATA_DIR/test-data.mat outputName ~/wkdir/best-190729/test-1 memMethod cMEM sensorsType EEG+MEG reconstructionWindow "0.7 0.71" baselineWindow "0 0.5"'

Check for the output file test-1.mat.