Added an option to define the path of the singularity executable

docs/getting_started/user-guide.rst

@@ -203,6 +203,11 @@ variable replacement. A summary table of variables is included below, and then f
    * - singularity_module
      - if defined, add to module script to load this Singularity module first
      - null
+   * - podman_module
+     - if defined, add to module script to load this Podman module first
+     - null
+   * - singularity_path
+     - path to (or name of) the `singularity` executable to use in wrapper scripts. Can be used instead of / with `singularity_module`
    * - module_name
      - Format string for module commands exec,shell,run (not aliases) can include ``{{ registry }}``, ``{{ repository }}``, ``{{ tool }}`` and ``{{ version }}``
      - ``'{{ tool }}'``

shpc/main/schemas.py

@@ -143,6 +143,7 @@
     "namespace": {"type": ["string", "null"]},
     "singularity_module": {"type": ["string", "null"]},
     "podman_module": {"type": ["string", "null"]},
+    "singularity_path": {"type": ["string"]},
     "bindpaths": {"type": ["string", "null"]},
     "updated_at": {"type": "string"},
     "module_name": {"type": "string"},

shpc/main/wrappers/templates/singularity/exec.sh

@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}{{ settings.singularity_path }} ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}

shpc/main/wrappers/templates/singularity/inspect-deffile.sh

@@ -1,3 +1,3 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} -d {{ image }}{% endblock %}
+{% block content %}{{ settings.singularity_path }} ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} -d {{ image }}{% endblock %}

shpc/main/wrappers/templates/singularity/inspect-runscript.sh

@@ -1,3 +1,3 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} -r {{ image }}{% endblock %}
+{% block content %}{{ settings.singularity_path }} ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} -r {{ image }}{% endblock %}

shpc/main/wrappers/templates/singularity/run.sh

@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
+{% block content %}{{ settings.singularity_path }} ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} {% if alias.singularity_options %} {{ alias.singularity_options }} {% endif %} {{ image }} {% if '/sh' in settings.wrapper_shell or '/bash' in settings.wrapper_shell %}"$@"{% elif '/csh' in settings.wrapper_shell %}$argv:q{% endif %}
 {% endblock %}

shpc/main/wrappers/templates/singularity/shell.sh

@@ -1,4 +1,4 @@
 {% extends "bases/shell-script-base.sh" %}
 
-{% block content %}singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} -s {{ settings.wrapper_shell }} {{ image }}
+{% block content %}{{ settings.singularity_path }} ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if settings.environment_file %}-B $wrapperDir/{{ settings.environment_file }}:/.singularity.d/env/{{ settings.environment_file }}{% endif %} {% if settings.bindpaths %}-B {{ settings.bindpaths }}{% endif %} -s {{ settings.wrapper_shell }} {{ image }}
 {% endblock %}

shpc/settings.yml

@@ -57,6 +57,9 @@ default_view:
 singularity_module:
 podman_module:
 
+# Path to (or name of) the singularity executable to use in wrapper scripts. Can be used instead of / with singularity_module
+singularity_path: singularity
+
 # string with comma separated list of paths to binds. If set, expored to SINGULARITY_BINDPATH
 bindpaths: