Merge pull request #769 from thomshaw92/master

New files for Micapipe

recipes/micapipe/README.md

@@ -1,19 +1,25 @@
 
 ----------------------------------
-## micapipe/0.1.2 ##
-Short_description_of_container
+## micapipe/toolVersion ##
+Micapipe is a processing pipeline providing a robust framework to analyze multimodal MRI data. This pipeline integrates processing streams for T1-weighted, microstructure-sensitive, diffusion-weighted, and resting-state functional imaging to facilitate the development of multiscale models of neural organization. For this purpose, we leverage several specialized software packages to bring BIDS-formatted raw MRI data to fully-processed surface-based feature matrices.
 
 Example:
 ```
+micapipe -h
 ```
 
-More documentation can be found here: link_to_documentation
+More documentation can be found here: (https://micapipe.readthedocs.io/en/latest/pages/01.whatyouneed/index.html)
 
-To run applications outside of this container: ml micapipe/0.1.2 
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml micapipe/toolVersion
 
 Citation:
 ```
 
+Raúl R. Cruces, Jessica Royer, Peer Herholz, Sara Larivière, Reinder Vos de Wael, Casey Paquola, Oualid Benkarim, Bo-yong Park, Janie Degré-Pelletier, Mark Nelson, Jordan DeKraker, Ilana Leppert, Christine Tardif, Jean-Baptiste Poline, Luis Concha, Boris C. Bernhardt. (2022). Micapipe: a pipeline for multimodal neuroimaging and connectome analysis. NeuroImage, 2022, 119612, ISSN 1053-8119. doi: https://doi.org/10.1016/j.neuroimage.2022.119612
+
 ```
 
+License: 
+Copyright 2022, micapipe Revision c403161d.
+
 ----------------------------------

recipes/micapipe/build.sh

@@ -1,33 +1,27 @@
-
-#!/usr/bin/env bash
-
-#Micapipe neurodocker file taken from https://github.com/MICA-MNI/micapipe/blob/master/generate_micapipe_images.sh 
-#and edited to fit neurodesk
-
-set -e
-
 export toolName='micapipe'
-export toolVersion='v0.1.2'
+export toolVersion='v0.2.3' 
+# check if version is here: https://hub.docker.com/r/micalab/micapipe/tags
 # Don't forget to update version change in README.md!!!!!
-
 if [ "$1" != "" ]; then
-    echo "Entering Debug mode"
-    export debug=$1
+   echo "Entering Debug mode"
+   export debug=$1
 fi
-
 source ../main_setup.sh
 
-# Generate Dockerfile.
 neurodocker generate ${neurodocker_buildMode} \
    --base-image micalab/${toolName}:${toolVersion} \
    --pkg-manager apt \
    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
    --run="chmod +x /usr/bin/ll" \
    --run="mkdir -p ${mountPointList}" \
+   --workdir /opt \
+   --install wget git curl ca-certificates unzip \
+   --env PATH='$PATH':/opt/${toolName}-${toolVersion}/bin \
+   --env DEPLOY_PATH=/opt/${toolName}-${toolVersion}/bin/ \
    --copy README.md /README.md \
-  > ${imageName}.${neurodocker_buildExt}
-
-  
+   --copy test.sh /test.sh \
+   --run="bash /test.sh" \
+> ${imageName}.${neurodocker_buildExt}
 
 if [ "$1" != "" ]; then
    ./../main_build.sh

recipes/micapipe/test.sh

@@ -1 +1 @@
-# this file should contain a functional test of the tool that makes it possible to test if everything was correctly installed
+micapipe --help