bugfix

takuma-yoneda · Dec 24, 2023 · abd1f73 · abd1f73
1 parent fd995b3
commit abd1f73
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/lmn/container/singularity.py b/lmn/container/singularity.py
@@ -38,8 +38,7 @@ def run(cmd: str, singularity_config: SingularityConfig) -> str:
         options = SingularityCommand.make_options(c)
 
         if c.startup:
-            if isinstance(c.startup, list):
-                startup = " ; ".join(c.startup)
+            startup = " ; ".join(c.startup) if isinstance(c.startup, list) else c.startup
             cmd = f"{startup} ; {cmd}"
         # Escape special chars and quotes (https://stackoverflow.com/a/18886646/19913466)
         logger.debug(f"cmd before escape: {cmd}")

diff --git a/lmn/runner.py b/lmn/runner.py
@@ -370,7 +370,7 @@ def exec(self, cmd: str, relative_workdir, conf: PBSConfig, env: Optional[dict]
         exec_str = '\n'.join((
             # NOTE: without `-S` option, `bash -i` will be considered a single command and will end up in command not found.
             # Reference: https://unix.stackexchange.com/a/657774/556831
-            '#!/usr/bin/env -S bash -i',
+            '#!/usr/bin/env -S bash -i' if interactive else '#!/usr/bin/env bash',
             *slurm_options,
             *exports,
             cmd