From 5e49a4be1866dea06d35d4c0a8004f8ccf9dd19e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 9 Apr 2026 12:27:29 -0500
Subject: Specify the --permu_output option to QTLReaper

Specify the --permu_output option to QTLReaper to prevent it from
attempting to write to the working directory, which in the guix
containers is a READONLY file system.
---
 scripts/run_qtlreaper.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py
index b9ccaa5..5ab5b21 100644
--- a/scripts/run_qtlreaper.py
+++ b/scripts/run_qtlreaper.py
@@ -147,13 +147,16 @@ def dispatch(args: Namespace) -> int:
 
             _qtlreaper_main_output = args.working_dir.joinpath(
                 f"main-output-{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined]
+            _qtlreaper_permu_output = args.working_dir.joinpath(
+                f"permu-output-{secrets.token_urlsafe(15)}.tsv")
             logger.debug("Main output filename: %s", _qtlreaper_main_output)
             with subprocess.Popen(
                     ("qtlreaper",
                      "--n_permutations", "1000",
                      "--geno", _genofile,
                      "--traits", _traitsfile,
-                     "--main_output", _qtlreaper_main_output),
+                     "--main_output", _qtlreaper_main_output,
+                     "--permu_output", _qtlreaper_permu_output),
                     env=({**os.environ, "RUST_BACKTRACE": "full"}
                          if logger.getEffectiveLevel() == logging.DEBUG
                          else dict(os.environ))) as _qtlreaper:
@@ -178,7 +181,11 @@ def dispatch(args: Namespace) -> int:
 
             if _qtlreaper_main_output.exists():
                 _qtlreaper_main_output.unlink()
-                logger.info("Deleted QTLReaper output file.")
+                logger.info("Deleted QTLReaper's main output file.")
+
+            if _qtlreaper_permu_output.exists():
+                _qtlreaper_permu_output.unlink()
+                logger.info("Deleted QTLReaper's permutations file.")
 
             if _qtlreaper.returncode != 0:
                 return _qtlreaper.returncode
-- 
cgit 1.4.1