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| author | Pjotr Prins | 2024-04-03 12:26:35 +0200 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-09-12 07:40:04 -0500 |
| commit | e10b62f88432856019540074fd19b6acdb70d4ad (patch) | |
| tree | 63dbd35a04d359229a69645f623d659ba1f37f4c | |
| parent | fd25b6bf205e4642cf5f6ba5ed0e0cad73efc0b6 (diff) | |
| download | genenetwork3-e10b62f88432856019540074fd19b6acdb70d4ad.tar.gz | |
Modify script paths so they can be edited in Guix
| -rw-r--r-- | gn3/computations/ctl.py | 2 | ||||
| -rw-r--r-- | gn3/computations/wgcna.py | 2 |
2 files changed, 2 insertions, 2 deletions
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 |