Make ImageMagick convert findable in SLURM array workers#3
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The batch `convert`/`rename` jobs are written as plain `#!/bin/sh` scripts
and submitted as a SLURM array; those workers do not activate any conda
environment, so a bare `convert` was not on PATH on the compute nodes and
every task failed with exit code 127 ("command not found").
Prepend the running interpreter's bin directory (from sys.executable) to
PATH in each generated worker script, so tools installed alongside it
(e.g. ImageMagick) are found by the workers.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Problem
The batch convert/rename actions are written as plain /bin/sh scripts and submitted as a SLURM job array (submit_to_slurm). Those array workers run under /bin/sh without activating any conda environment, so a bare 'convert' is not on PATH on the compute nodes. Every array task fails immediately with exit code 127 (command not found) and no output is produced -- observed on the PelkmansLab HPC cluster after a storage migration removed the system-wide ImageMagick the workers had relied on.
Fix
Prepend the running interpreter's bin directory (derived from sys.executable) to PATH in each generated worker script, so tools installed alongside the Python interpreter that runs mf.py (e.g. ImageMagick's convert) are found by the /bin/sh workers -- without hard-coding any environment path.
Notes