From 039c1dee9add8f784911a84c7a5f16915166ba93 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 19 Feb 2024 02:23:29 +0000
Subject: Pass qtlreaper command path as argument to run_reaper

Originally the system would get the path from the environment
---
 gn3/computations/qtlreaper.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 981a9c8..8c970f2 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -7,7 +7,7 @@ import subprocess
 from typing import Union
 
 from gn3.chancy import random_string
-from gn3.settings import TMPDIR, REAPER_COMMAND
+from gn3.settings import TMPDIR
 
 def generate_traits_file(samples, trait_values, traits_filename):
     """
@@ -39,6 +39,7 @@ def create_output_directory(path: str):
         pass
 
 def run_reaper(
+        reaper_cmd: str,
         genotype_filename: str, traits_filename: str,
         other_options: tuple = ("--n_permutations", "1000"),
         separate_nperm_output: bool = False,
@@ -81,7 +82,7 @@ def run_reaper(
         permu_output_filename = None
 
     command_list = [
-        REAPER_COMMAND, "--geno", genotype_filename,
+        reaper_cmd, "--geno", genotype_filename,
         *other_options, # this splices the `other_options` list here
         "--traits", traits_filename,
         *output_list # this splices the `output_list` list here
-- 
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