NF: SINGULARITY_CMD env var to override default "run" with e.g. "exec"

README.md provides more details but the main use case to overcome hardcodeness
of which command to use (run) in singularity invocation.  It opens the door for
using  containers-run  in interactive sessions with containers which configured
for execution of main entry point commands, e.g.

    SINGULARITY_CMD=exec datalad containers-run -n repronim-reproin bash

Author: yarikoptic

README.md

@@ -64,6 +64,24 @@ so we just use uniform `.sing` extension.
 		data/bids {outputs} participant
 
 
+## Environment variables
+
+A few environment variables (in addition to those consulted by datalad
+and datalad-container) are considered in the scripts of this
+repository:
+
+### `SINGULARITY_CMD`
+
+The default command (as "hardcoded" in [.datalad/config][]) is `run`
+so running the container executes its default "entry point".  Setting
+`SINGULARITY_CMD=exec` makes it possible to run an alternative command
+in them (e.g. `bash` for interactive sessions)::
+
+    SINGULARITY_CMD=exec datalad containers-run --explicit -n repronim-reproin bash
+
+and then have `datalad` record any of the introduced changes.  Such
+runs will not be reproducible but at least clearly annotated in what
+environment corresponding actions were taken.
 
 [git-annex]: http://git-annex.branchable.com
 [DataLad]: http://datalad.org

scripts/singularity_cmd

@@ -40,7 +40,7 @@ function info() {
 thisdir=$(dirname $0| xargs readlink -f)
 updir=$(dirname "$thisdir")
 
-cmd="$1"; shift
+cmd="${SINGULARITY_CMD:-$1}"; shift
 
 if [ ! -z "${DATALAD_CONTAINER_NAME:-}" ]; then
 	export SINGULARITYENV_DATALAD_CONTAINER_NAME="$DATALAD_CONTAINER_NAME"