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Release 2.1.0 #403

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Merged
sivkovic merged 5 commits into from
Mar 24, 2026
Merged

Release 2.1.0 #403

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74bc28c
use map for legacy app environments
buehlere Mar 17, 2026
a7948a1
format
buehlere Mar 17, 2026
700cebb
Merge pull request #400 from mskcc/feature/flexible_execution_env
buehlere Mar 17, 2026
545b14d
Version bump 2.1.0
sivkovic Mar 19, 2026
56a7c96
Merge branch 'master' of github.com:mskcc/ridgeback into release/2.1.0
sivkovic Mar 24, 2026
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2 changes: 1 addition & 1 deletion ridgeback/__init__.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "2.0.0"
__version__ = "2.1.0"
14 changes: 11 additions & 3 deletions ridgeback/settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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, ...)
Expand Down Expand Up @@ -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"
7 changes: 5 additions & 2 deletions submitter/toil_submitter/toil_jobsubmitter.py
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Expand Up @@ -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):
Expand Down
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