Get cytoscape running with config mechanism

Snakefile

@@ -247,7 +247,7 @@ rule viz_cytoscape:
     output: 
         session = SEP.join([out_dir, '{dataset}-cytoscape.cys'])
     run:
-        cytoscape.run_cytoscape(input.pathways, output.session, SINGULARITY)
+        cytoscape.run_cytoscape(input.pathways, output.session)
 
 
 # Write a single summary table for all pathways for each dataset

src/analysis/cytoscape.py

@@ -2,10 +2,12 @@
 from shutil import rmtree
 from typing import List, Union
 
-from src.util import prepare_volume, run_container
+import src.config as config
+from src.containers import run_container
+from src.util import prepare_volume
 
 
-def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, singularity: bool = False) -> None:
+def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str) -> None:
     """
     Create a Cytoscape session file with visualizations of each of the provided pathways
     @param pathways: a list of pathways to visualize
@@ -49,9 +51,10 @@ def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, singul
     print('Running Cytoscape with arguments: {}'.format(' '.join(command)), flush=True)
 
     # TODO consider making this a string in the config file instead of a Boolean
-    container_framework = 'singularity' if singularity else 'docker'
+    container_framework = config.config.container_framework
+    container_prefix = "py4cytoscape:v1"
     out = run_container(container_framework,
-                        'reedcompbio/py4cytoscape:v1',
+                        container_prefix,
                         command,
                         volumes,
                         work_dir,

test/analysis/test_cytoscape.py

@@ -3,6 +3,7 @@
 
 import pytest
 
+import src.config as config
 from src.analysis.cytoscape import run_cytoscape
 
 INPUT_DIR = 'test/analysis/input/example/'
@@ -33,7 +34,9 @@ def test_cytoscape(self):
     # Open a GitHub issue if Cytoscape does not work on Singularity as expected for assistance debugging
     @pytest.mark.xfail(reason='Requires Singularity and only works for certain Singularity configurations')
     def test_cytoscape_singularity(self):
+        config.config.container_framework = "singularity"
         out_path = Path(OUT_FILE)
         out_path.unlink(missing_ok=True)
-        run_cytoscape(INPUT_PATHWAYS, OUT_FILE, True)
+        run_cytoscape(INPUT_PATHWAYS, OUT_FILE)
+        config.config.container_framework = "docker"
         assert out_path.exists()