htcondorcern: commands are not run in provided unpacked images

[mdonadoni]

Consider the following changes to reana-demo-helloworld:

--- a/workflow/snakemake/Snakefile
+++ b/workflow/snakemake/Snakefile
@@ -25,10 +25,14 @@ rule helloworld:
         sleeptime=config["sleeptime"]
     output:
         "results/greetings.txt"
-    container:
-        "docker://docker.io/library/python:2.7-slim"
+    resources:
+        kerberos=True,
+        compute_backend="htcondorcern",
+        htcondor_max_runtime="espresso",
+        unpacked_img=True
+    container: "/cvmfs/unpacked.cern.ch/registry.hub.docker.com/rootproject/root:6.26.00-ubuntu20.04"
     shell:
-        "python {input.helloworld} "
-        "--inputfile {input.inputfile} "
-        "--outputfile {output} "
-        "--sleeptime {params.sleeptime}"
+        """
+echo $SINGULARITY_NAME ;
+python --version
+        """

When executing this job, reana-job-controller will create the following job_singularity_wrapper.sh wrapper to run the user-provided commands on HTCondor:

#!/bin/bash 
singularity exec --home $PWD:/srv --bind $PWD:/srv --bind /cvmfs --bind /eos /cvmfs/unpacked.cern.ch/registry.hub.docker.com/rootproject/root:6.26.00-ubuntu20.04  echo ZWNobyAkU0lOR1VMQVJJVFlfTkFNRSA7IHB5dGhvbiAtLXZlcnNpb24=|base64 -d | bash

Note that:

$  echo ZWNobyAkU0lOR1VMQVJJVFlfTkFNRSA7IHB5dGhvbiAtLXZlcnNpb24=|base64 -d
echo $SINGULARITY_NAME ; python --version

However, if we execute this script manually on lxplus, this is the output:

$ bash job_singularity_wrapper.sh 

bash: line 1: python: command not found

The | base64 -d | bash part of the script is not executed in the singularity container, but in the outer bash shell, thus the user-provided commands are not executed in the singularity container.