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Added an option to define the path of the singularity executable #689

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Merged
merged 3 commits into from
Apr 11, 2025
Merged

Added an option to define the path of the singularity executable #689

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ebe6584
Missing doc
muffato Oct 3, 2023
12e547a
Added an option to configure the path to singularity directly
muffato Oct 3, 2023
be578c0
Bumped the version number and updated the changelog
muffato Apr 10, 2025
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Added an option to configure the path to singularity directly
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@muffato
muffato committed Apr 9, 2025
commit 12e547a7501944501a63570699abcbf13921dff6
2 changes: 2 additions & 0 deletions docs/getting_started/user-guide.rst
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Expand Up @@ -206,6 +206,8 @@ variable replacement. A summary table of variables is included below, and then f
* - podman_module
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@vsoch vsoch Apr 9, 2025

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Should podman module be here? The singularity path addition is fantastic - great for security too.

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@muffato muffato Apr 10, 2025

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Yes, I noticed it was missing from the doc and thought I'd squeeze that in :)

- 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 }}'``
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1 change: 1 addition & 0 deletions shpc/main/schemas.py
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Expand Up @@ -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"},
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2 changes: 1 addition & 1 deletion shpc/main/wrappers/templates/singularity/exec.sh
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{% 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 %}
2 changes: 1 addition & 1 deletion shpc/main/wrappers/templates/singularity/inspect-deffile.sh
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{% 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 %}
2 changes: 1 addition & 1 deletion shpc/main/wrappers/templates/singularity/inspect-runscript.sh
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{% 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 %}
2 changes: 1 addition & 1 deletion shpc/main/wrappers/templates/singularity/run.sh
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{% 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 %}
2 changes: 1 addition & 1 deletion shpc/main/wrappers/templates/singularity/shell.sh
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{% 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 %}
3 changes: 3 additions & 0 deletions shpc/settings.yml
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Expand Up @@ -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:

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