From ded0728505455c80b1f2a042b6b3c13dc0b27e9c Mon Sep 17 00:00:00 2001 From: jakevc Date: Mon, 15 Jul 2024 15:35:37 -0700 Subject: [PATCH] override real.py --- snakemake_executor_plugin_azure_batch/__init__.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/snakemake_executor_plugin_azure_batch/__init__.py b/snakemake_executor_plugin_azure_batch/__init__.py index 5d3e2a3..c5a1099 100644 --- a/snakemake_executor_plugin_azure_batch/__init__.py +++ b/snakemake_executor_plugin_azure_batch/__init__.py @@ -288,6 +288,19 @@ def __post_init__(self): self.create_batch_pool() self.create_batch_job() + # override real.py until bugfix is released + def get_envvar_declarations(self): + if self.common_settings.pass_envvar_declarations_to_cmd: + defs = " ".join( + f"{var}={repr(value)}" for var, value in self.envvars.items() + ) + if defs: + return f"export {defs} &&" + else: + return "" + else: + return "" + def init_batch_client(self): """ Initialize the batch service client from the given credentials