diff --git a/ridgeback/__init__.py b/ridgeback/__init__.py index 8c0d5d5b..9aa3f903 100644 --- a/ridgeback/__init__.py +++ b/ridgeback/__init__.py @@ -1 +1 @@ -__version__ = "2.0.0" +__version__ = "2.1.0" diff --git a/ridgeback/settings.py b/ridgeback/settings.py index 666e1ae5..29d88539 100644 --- a/ridgeback/settings.py +++ b/ridgeback/settings.py @@ -10,6 +10,7 @@ https://docs.djangoproject.com/en/2.2/ref/settings/ """ +import json import os # Build paths inside the project like this: os.path.join(BASE_DIR, ...) @@ -326,9 +327,16 @@ SKIP_THE_QUEUE_JOBS = ("ARGOS", "ACCESS_HEME", "ACCESS", "CMO-CH") # ACCESS LEGACY INFO -ACCESS_LEGACY_APP = os.environ.get("ACCESS_LEGACY_APP", "access-pipeline") -ACCESS_LEGACY_CONDA_ENV = os.environ.get( - "ACCESS_LEGACY_CONDA_ENV", "/usersoftware/core005/access/production/V1/micromamba/envs/ACCESS-voyager/bin" +ACCESS_LEGACY_APP_ENV_MAP = json.loads( + os.environ.get( + "ACCESS_LEGACY_APP_ENV_MAP", + json.dumps( + { + "access-pipeline": "/usersoftware/core005/access/production/V1/micromamba/envs/ACCESS-voyager/bin", + "access_heme": "/usersoftware/core005/accessH/development/envs/ACCESS-HEME-voyager/bin", + } + ), + ) ) SHELL_PLUS = "ipython" diff --git a/submitter/toil_submitter/toil_jobsubmitter.py b/submitter/toil_submitter/toil_jobsubmitter.py index bffa2ace..b64f7eda 100644 --- a/submitter/toil_submitter/toil_jobsubmitter.py +++ b/submitter/toil_submitter/toil_jobsubmitter.py @@ -89,8 +89,11 @@ def get_submit_command(self): env["TMP"] = self.job_tmp_dir env["TMPDIR"] = self.job_tmp_dir env[self.batch_system_args_env] = toil_batch_system_args.strip() - if settings.ACCESS_LEGACY_APP in self.app.github.lower(): - env["PATH"] = f"{settings.ACCESS_LEGACY_CONDA_ENV}:{os.environ.get('PATH')}" + github_lower = self.app.github.lower() + for app_key, conda_env in settings.ACCESS_LEGACY_APP_ENV_MAP.items(): + if app_key in github_lower: + env["PATH"] = f"{conda_env}:{os.environ.get('PATH')}" + break return command_line, self._leader_args(), log_path, self.job_id, self.partition, env def get_commandline_status(self, cache):