diff --git a/test/workflow/module_tests/no_docker_test_cggnn.sh b/test/workflow/module_tests/no_docker_test_cggnn.sh index c95f5d159..2e6c1318f 100755 --- 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/