3. Test installation

We recommend to test that all dependencies were properly installed (particularly if you used Option 3).

• If you used Option 1 (singularity), you can type:

  mkdir perSVade_testing_outputs

  singularity exec -B ./perSVade_testing_outputs:/perSVade/installation/test_installation/testing_outputs -e mikischikora_persvade_<tag>.sif bash -c 'source /opt/conda/etc/profile.d/conda.sh && conda activate perSVade_env && /perSVade/installation/test_installation/test_installation_modules.py'

  Note that the script test_installation_modules.py would write data into /perSVade/installation/test_installation/testing_outputs inside the container by default. However, we cannot write files inside the singularity container in the way that we built it (for reproducibility reasons). Using -B is a solution for this: it specifies a mounting of the /perSVade/installation/test_installation/testing_outputs of the container into ./perSVade_testing_outputs of the host machine (where the data will be written in a persistent way). If you encounter environmental errors here, check this FAQ.

• If you used Option 2 (docker), you can type:

  mkdir perSVade_testing_outputs

  docker run -v $PWD/perSVade_testing_outputs:/perSVade/installation/test_installation/testing_outputs mikischikora/persvade:<tag> python -u ./installation/test_installation/test_installation_modules.py

  Note that the script test_installation_modules.py writes data into /perSVade/installation/test_installation/testing_outputs inside the container. Without the -v option, this data would be lost once the docker run command was finished, as the container is destroyed. The argument -v $PWD/perSVade_testing_outputs:/perSVade/installation/test_installation/testing_outputs (with the format -v <path in host>:<path in container> and full paths) allows the data to persist in the ./perSVade_testing_outputs of the host machine.

• If you used Option 3 (traditional), you can use conda activate <env_name> && ./installation/test_installation/test_installation_modules.py

This process should take around 45 minutes on 4 cores. The docker and singularity runs on Mac or Winows OS may be slower. Verify that it finishes with the following message:

SUCCESS: perSVade was properly installed