add heudiconv

recipes/heudiconv/README.md

@@ -0,0 +1,22 @@
+
+----------------------------------
+## heudiconv/1.3.1 ##
+heudiconv is a flexible DICOM converter for organizing brain imaging data into structured directory layouts.
+
+Example:
+```
+heudiconv  --files dicom/219/itbs/*/*.dcm -o Nifti -f Nifti/code/heuristic1.py -s 219 -ss itbs -c dcm2niix -b --minmeta --overwrite
+```
+
+More documentation can be found here: https://heudiconv.readthedocs.io/en/latest/quickstart.html
+
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml heudiconv/1.3.1
+
+Citation:
+```
+Halchenko, Yaroslav O., Mathias Goncalves, Satrajit Ghosh, Pablo Velasco, Matteo Visconti Di Oleggio Castello, Taylor Salo, John T. Wodder Ii, et al. “HeuDiConv — Flexible DICOM Conversion into Structureddirectory Layouts.” Journal of Open Source Software 9, no. 99 (July 3, 2024): 5839. https://doi.org/10.21105/joss.05839.
+```
+
+License: Apache License, Version 2.0
+
+----------------------------------

recipes/heudiconv/build.sh

@@ -0,0 +1,26 @@
+export toolName='heudiconv'
+export toolVersion='1.3.1' 
+# https://hub.docker.com/r/nipy/heudiconv/tags
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+source ../main_setup.sh --reinstall_neurodocker=false
+
+neurodocker generate ${neurodocker_buildMode} \
+   --base-image nipy/heudiconv:$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=heudiconv \
+   --copy README.md /README.md \
+   --copy test.sh /test.sh \
+  > ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi

recipes/heudiconv/test.sh

@@ -0,0 +1 @@
+heudiconv

recipes/template_minimal/build.sh

@@ -5,7 +5,7 @@ if [ "$1" != "" ]; then
     echo "Entering Debug mode"
     export debug=$1
 fi
-source ../main_setup.sh
+source ../main_setup.sh --reinstall_neurodocker=false
 
 neurodocker generate ${neurodocker_buildMode} \
    --base-image neurodebian:sid-non-free \