Add shebang to fix slurm support

Donders-Institute · Oct 27, 2023 · 3a84008 · 3a84008
1 parent ee9b932
commit 3a84008
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/bidscoin/bidsapps/skullstrip.py b/bidscoin/bidsapps/skullstrip.py
@@ -113,9 +113,9 @@ def skullstrip(bidsdir: str, pattern: str, subjects: list, masked: str, output:
                     maskimg.parent.mkdir(parents=True, exist_ok=True)
                     command = f"mri_synthstrip -i {srcimg} -o {outputimg} -m {maskimg} {args}"
                     if cluster == 'torque':
-                        command = f"qsub -l walltime=0:05:00,mem=8gb -N skullstrip_{subid}_{sesid} << EOF\n{command}\nEOF"
+                        command = f"qsub -l walltime=0:05:00,mem=8gb -N skullstrip_{subid}_{sesid} << EOF\n#!/bin/bash\n{command}\nEOF"
                     elif cluster == 'slurm':
-                        command = f"sbatch --time=0:05:00 --mem=8G --job-name=skullstrip_{subid}_{sesid} << EOF\n{command}\nEOF"
+                        command = f"sbatch --time=0:05:00 --mem=8G --job-name=skullstrip_{subid}_{sesid} << EOF\n#!/bin/bash\n{command}\nEOF"
                     elif cluster:
                         LOGGER.error(f"Invalid cluster manager `{cluster}`")
                         exit(1)

diff --git a/bidscoin/bidsapps/slicereport.py b/bidscoin/bidsapps/slicereport.py
@@ -88,9 +88,9 @@ def slicer_append(inputimage: Path, outlineimage: Path, mainopts: str, outputopt
     # Wrap the command
     mem = '8' if inputimage.stat().st_size > 50 * 1024**2 else '1'  # Ask for more resources if we have a large (e.g. 4D) input image
     if cluster == 'torque':
-        command = f"qsub -l walltime=0:02:00,mem={mem}gb -N slicereport -e {tempfile.gettempdir()} -o {tempfile.gettempdir()} << EOF\n{command}\nEOF"
+        command = f"qsub -l walltime=0:02:00,mem={mem}gb -N slicereport -e {tempfile.gettempdir()} -o {tempfile.gettempdir()} << EOF\n#!/bin/bash\n{command}\nEOF"
     elif cluster == 'slurm':
-        command = f"sbatch --time=0:02:00 --mem={mem}G --job-name slicereport -o {tempfile.gettempdir()}/slurm-%j.out << EOF\n{command}\nEOF"
+        command = f"sbatch --time=0:02:00 --mem={mem}G --job-name slicereport -o {tempfile.gettempdir()}/slurm-%j.out << EOF\n#!/bin/bash\n{command}\nEOF"
     elif cluster:
         LOGGER.error(f"Invalid cluster manager `{cluster}`")
         exit(1)