use virtualenv

nadeemlab · Dec 15, 2023 · ca0d541 · ca0d541
1 parent e305119
commit ca0d541
Showing 1 changed file with 7 additions and 4 deletions.
diff --git a/test/workflow/module_tests/no_docker_test_cggnn.sh b/test/workflow/module_tests/no_docker_test_cggnn.sh
@@ -1,5 +1,7 @@
-# Set up a virtual environment to run this test and install SPT in it.
-# TODO
+# Set up a virtual environment to run this test
+python -m venv env
+source env/bin/activate
+pip install ../../..
 
 # Run the workflow
 spt workflow configure --local --workflow='cggnn' --study-name='Melanoma intralesional IL2' --database-config-file=../db/.spt_db.config.container --workflow-config-file=module_tests/.workflow.config
@@ -66,5 +68,6 @@ else
 fi
 
 # Clean up
-rm -f .nextflow.log*; rm -rf .nextflow/; rm -f configure.sh; rm -f run.sh; rm -f main.nf; rm -f nextflow.config; rm top_100_structures.txt; rm top_100_reference.txt; # rm -rf results/
-# TODO: Delete the virtual environment this test ran in
+rm -f .nextflow.log*; rm -rf .nextflow/; rm -f configure.sh; rm -f run.sh; rm -f main.nf; rm -f nextflow.config; rm -f top_100_structures.txt; rm -f top_100_reference.txt; rm -rf results/
+deactivate
+rm -rf env/