Prototype of a neurodocker invocation script to produce a container

It is not yet finished
- did not even try FSL installation
- AFNI installation relies on incomplete fixes proposed in
  ReproNim/neurodocker#601
- moved away attempt to install bids-validator (would be useful) due
  those failing too ATM

generate_container.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+set -eu
+
+generate() {
+	# more details might come on https://github.com/ReproNim/neurodocker/issues/330
+	[ "$1" == singularity ] && add_entry=' "$@"' || add_entry=''
+	#neurodocker generate "$1" \
+	ndversion=0.9.5
+	#ndversion=master
+	#docker run --rm repronim/neurodocker:$ndversion \
+    # ATM needs devel version  of neurodocker for a fix to AFNI recipe
+    neurodocker \
+        generate "$1" \
+		--base-image neurodebian:bookworm \
+		--ndfreeze date=20240320 \
+		--copy environment.yml /opt/environment.yml \
+        --miniconda \
+            version=latest \
+            env_name=dsstdeface \
+            env_exists=false \
+            yaml_file=/opt/environment.yml \
+		--pkg-manager=apt \
+		--install vim wget strace time ncdu gnupg curl procps pigz less tree \
+		--run "apt-get update && apt-get -y dist-upgrade" \
+        --afni method=binaries version=latest \
+		--user=dsst \
+		--entrypoint "bash"
+		#--run "curl -sL https://deb.nodesource.com/setup_16.x | bash - " \
+		#--install nodejs npm \
+		#--run "npm install -g [email protected]" \
+        #--fsl version=6.0.7.1 \
+}
+
+generate docker > Dockerfile
+# generate singularity > Singularity