From e10b62f88432856019540074fd19b6acdb70d4ad Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 3 Apr 2024 12:26:35 +0200
Subject: Modify script paths so they can be edited in Guix

---
 gn3/computations/ctl.py   | 2 +-
 gn3/computations/wgcna.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn3')

diff --git a/gn3/computations/ctl.py b/gn3/computations/ctl.py
index f881410..eb34656 100644
--- a/gn3/computations/ctl.py
+++ b/gn3/computations/ctl.py
@@ -13,7 +13,7 @@ def call_ctl_script(data):
     """function to call ctl script"""
     data["imgDir"] = TMPDIR
     temp_file_name = dump_wgcna_data(data)
-    cmd = compose_wgcna_cmd("ctl_analysis.R", temp_file_name)
+    cmd = compose_wgcna_cmd("scripts/ctl_analysis.R", temp_file_name)
 
     cmd_results = run_cmd(cmd)
     with open(temp_file_name, "r", encoding="utf-8") as outputfile:
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index c985491..01d024b 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -58,7 +58,7 @@ def process_image(image_loc: str) -> bytes:
 def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
     """function to componse wgcna cmd"""
     # (todo):issue relative paths to abs paths
-    cmd = f"Rscript ./scripts/{rscript_path}  {temp_file_path}"
+    cmd = f"Rscript scripts/{rscript_path} {temp_file_path}"
     return cmd
 
 
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