hard coded shell executable to bash for source commands, because sour…

…ce is not POSIX standard
NCI-CGR · Sep 8, 2023 · 8bfd534 · 8bfd534
1 parent ab19965
commit 8bfd534
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Showing 4 changed files with 7 additions and 14 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/src/cgr_gwas_qc/testing/conda.py b/src/cgr_gwas_qc/testing/conda.py
@@ -24,7 +24,6 @@
 
 
 class CondaEnv:
-
     conda_env_path = Path(__file__).absolute().parents[1] / "workflow/conda"
 
     def __init__(self, cache_path: Optional[Union[str, Path]] = None):
@@ -128,4 +127,6 @@ def _create_conda_env(self, env_file: str, build_path: str) -> None:
                 build_path,
             ]
         )
-        subprocess.run(cmd, shell=True, check=True, stderr=subprocess.STDOUT)
+        subprocess.run(
+            cmd, shell=True, check=True, stderr=subprocess.STDOUT, executable="/bin/bash"
+        )
diff --git a/src/cgr_gwas_qc/testing/data.py b/src/cgr_gwas_qc/testing/data.py
@@ -498,7 +498,9 @@ def _sync_data(self):
             ]
         )
         try:
-            subprocess.run(cmd, shell=True, check=True, stderr=subprocess.STDOUT)
+            subprocess.run(
+                cmd, shell=True, check=True, stderr=subprocess.STDOUT, executable="/bin/bash"
+            )
         except subprocess.SubprocessError:
             warn(
                 f"Could not connect to {user}@{server}:{remote_path}. To "

diff --git a/src/cgr_gwas_qc/workflow/scripts/median_idat_intensity.py b/src/cgr_gwas_qc/workflow/scripts/median_idat_intensity.py
@@ -15,7 +15,7 @@ def main(
 ):
     Rscript = Path(get_snakemake_conda_env(conda_env)) / "bin/Rscript"
     cmd = f"{Rscript} --vanilla {rscript} {sample_id} {red} {green} {outfile}"
-    sp.check_output(cmd, shell=True)
+    sp.check_output(cmd, shell=True, executable="/bin/bash")
 
 
 if __name__ == "__main__" and "snakemake" in locals():