add neurodock

recipes/neurodock/README.md

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+
+----------------------------------
+## neurodock/1.0.0 ##
+PyD is an installable Python package deisgned to perform pre- and post- processing of dMRI acquisitions.
+
+Example:
+```
+pydesigner -s --verbose \
+~/Dataset/DKI_B0.nii,~/Dataset/DKI_B1000.nii,~/Dataset/DKI_B2000.nii
+```
+
+More documentation can be found here: https://pydesigner.readthedocs.io/en/latest/processing/running_pyd.html
+
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml neurodock/1.0.0
+
+Citation:
+```
+Siddhartha Dhiman, Joshua B Teves, Kathryn E Thorn, Emilie T McKinnon,
+Hunter G Moss, Vitria Adisetiyo, Benjamin Ades-Aron, Jelle Veraart, Jenny Chen,
+Els Fieremans, Andreana Benitez, Joseph A Helpern, Jens H Jensen. PyDesigner: A
+Pythonic Implementation of the DESIGNER Pipeline for Diffusion Tensor and
+Diffusional Kurtosis Imaging. bioRxiv 2021.10.20.465189. doi:
+https://doi.org/10.1101/2021.10.20.465189```
+
+License: Custom license non-commerical, non-clinical care: https://github.com/muscbridge/PyDesigner?tab=License-1-ov-file#readme
+
+----------------------------------

recipes/neurodock/build.sh

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+export toolName='neurodock'
+export toolVersion='1.0.0' 
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+source ../main_setup.sh --reinstall_neurodocker=false
+
+neurodocker generate ${neurodocker_buildMode} \
+   --base-image dmri/neurodock:v${toolVersion} \
+   --env DEBIAN_FRONTEND=noninteractive \
+   --pkg-manager apt \
+   --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+   --run="chmod +x /usr/bin/ll" \
+   --run="mkdir -p ${mountPointList}" \
+   --env DEPLOY_BINS=pydesigner  \
+   --copy README.md /README.md \
+  > ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi