Merge pull request #904 from jnikhilreddy/update-hcpasl-recipe

hcpasl container recipe

recipes/hcpasl/README.md

@@ -0,0 +1,20 @@
+## hcpasl/1.0.0 ##
+HCP-ASL is a tool for processing ASL (Arterial Spin Labeling) data following the Human Connectome Project (HCP) minimal preprocessing pipelines. It provides a complete pipeline for processing ASL data, including motion correction, distortion correction, and calibration.
+
+The tool requires FSL, FreeSurfer, Workbench and HCP Pipelines as dependencies which are all included in this container.
+
+Example:
+```
+process_hcp_asl --help
+process_hcp_asl --subid ${Subjectid} --subdir ${SubDir} --mbpcasl ${mbpcasl} --fmap_ap ${SEFM_AP} --fmap_pa ${SEFM_PA} --grads ${GradientCoeffs}
+```
+
+More documentation can be found here: https://github.com/physimals/hcp-asl
+
+To run container outside of this environment: ml hcpasl/1.0.0
+
+Citation:
+```
+If you use HCP-ASL in your research, please cite:
+https://github.com/physimals/hcp-asl
+```

recipes/hcpasl/build.sh

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+#!/usr/bin/env bash
+set -e
+
+export toolName='hcpasl'
+export toolVersion='1.0.0'
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+# Auto-accept FSL license
+export ACCEPT_FSL_LICENSE=yes
+
+source ../main_setup.sh
+
+neurodocker generate ${neurodocker_buildMode} \
+   --base-image ubuntu:22.04 \
+   --pkg-manager apt \
+   --env DEBIAN_FRONTEND=noninteractive \
+   --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+   --run="chmod +x /usr/bin/ll" \
+   --run="mkdir -p ${mountPointList}" \
+   --install wget curl git \
+   --miniconda \
+      version=latest \
+      conda_install="python=3.11 numpy scipy" \
+      pip_install="git+https://github.com/physimals/hcp-asl.git nibabel" \
+   --fsl version=6.0.5.1 \
+   --freesurfer version=7.4.1 \
+   --install connectome-workbench \
+   --run="git clone https://github.com/Washington-University/HCPpipelines.git /opt/HCPpipelines" \
+   --env CARET7DIR=/usr/local/workbench/ \
+   --env HCPPIPEDIR=/opt/HCPpipelines \
+   --run="mkdir -p ${mountPointList}" \
+   --copy README.md /README.md \
+   --workdir /opt \
+   > ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi