diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/wgcna.py | 11 |
1 files changed, 7 insertions, 4 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index 01aaedb..ed7afc7 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -8,6 +8,7 @@ import base64 from gn3.settings import TMPDIR +from gn3.settings import R_SCRIPTS from gn3.commands import run_cmd @@ -55,16 +56,18 @@ def process_image(image_loc: str) -> bytes: return b"" -def compose_rscript_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}"' +def compose_rscript_cmd(script_path: str, + file_name: str, + temp_file_path: str): + + cmd = f'"Rscript {os.path.join(script_path,file_name)} {temp_file_path}"' return cmd def call_wgcna_script(rscript_path: str, request_data: dict): """function to call wgcna script""" generated_file = dump_wgcna_data(request_data) + cmd = compose_rscript_cmd(rscript_path, generated_file) # stream_cmd_output(request_data, cmd) disable streaming of data |