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add option to specify container resolver config file
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bernt-matthias committed Aug 22, 2023
1 parent 88994e6 commit 80f72d3
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Showing 2 changed files with 16 additions and 7 deletions.
3 changes: 2 additions & 1 deletion planemo/galaxy/config.py
Original file line number Diff line number Diff line change
Expand Up @@ -1394,7 +1394,8 @@ def _handle_container_resolution(ctx, kwds, galaxy_properties):
involucro_context = build_involucro_context(ctx, **kwds)
galaxy_properties["involucro_auto_init"] = "False" # Use planemo's
galaxy_properties["involucro_path"] = involucro_context.involucro_bin

if kwds.get("container_resolvers_config_file"):
galaxy_properties["container_resolvers_config_file"] = kwds.get("container_resolvers_config_file")

def _handle_job_metrics(config_directory, kwds):
metrics_conf = os.path.join(config_directory, "job_metrics_conf.xml")
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20 changes: 14 additions & 6 deletions planemo/options.py
Original file line number Diff line number Diff line change
Expand Up @@ -416,12 +416,20 @@ def tool_data_path_option():


def mulled_containers_option():
return planemo_option(
"mulled_containers",
"--mulled_containers",
"--biocontainers",
is_flag=True,
help="Test tools against mulled containers (requires --docker/--singularity, if none of these are given --docker is used automatically). Disables conda resolution unless any conda option has been set explicitly.",
return _compose(
planemo_option(
"mulled_containers",
"--mulled_containers",
"--biocontainers",
is_flag=True,
help="Test tools against mulled containers (requires --docker/--singularity, if none of these are given --docker is used automatically). Disables conda resolution unless any conda option has been set explicitly.",
),
planemo_option(
"--container_resolvers_config_file",
type=click.Path(exists=True, file_okay=True, dir_okay=False, resolve_path=True),
help="Container resolver config file",
default=None,
),
)


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