From 85b0be6c6f4298963baa4e80fa2daaac37c2952d Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed, 27 Mar 2024 16:52:27 -0400
Subject: [PATCH] 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
  https://github.com/ReproNim/neurodocker/pull/601
- moved away attempt to install bids-validator (would be useful) due
  those failing too ATM
---
 generate_container.sh | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100755 generate_container.sh

diff --git a/generate_container.sh b/generate_container.sh
new file mode 100755
index 0000000..a0081ef
--- /dev/null
+++ b/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 bids-validator@1.14.4" \
+		#--fsl version=6.0.7.1 \
+}
+
+generate docker > Dockerfile
+# generate singularity > Singularity