Installation

First, install conda environment. Mamba is preferred, but conda can be used as well (but will be slower).

conda env create -f environment.yml

Then, activate the environment:

conda activate idpp

Next, install pip dependencies:

pip install -r requirements.txt

Finally, manually install the following packages according to instructions in the home repos:

• DeepCCS

Retip dependencies will need to be installed in accordance with the instructions on https://www.retip.app/. Note that RTools is not required on non-Windows systems.

The above installation can be completed using sbatch/hpc_setup.sbatch if installing on Deception.

GrAFF-MS

To install and use GrAFF-MS, use the associated environment spec.

conda env create -f envs/graff-ms.yml

You can also use sbatch/graff-ms_setup.sbatch to install the environment on Deception.

Then you will need to manually configure the path to the GrAFF-MS repository. (Note: The repository paths specified in config/config.yaml should be correct and can be used as-is on Deception.)

Extra Installation Notes

• To install torch_scatter, first run module load gcc/<newest_version>
• Note that environment specs exist for many of the tools in the workflow, but the only tool requiring the user to pre-install its corresponding environment is GrAFF-MS (also DeepCCS requires the package to be installed in the main environment idpp).

HPC Instructions

HPC instructions are identical to the above, with the following changes for R packages specifically:

1. For R, make sure to load module load R/<newest version>
2. Load gcc: module load gcc/<newest version>
3. Load Java: module load java/1.8.0_31
4. Run R on the command line and install packages using the R commands in the Retip instructions.
5. Verify that /share/apps/R/<newest version>/bin is in your PATH variable with echo $PATH
   • If not, run export PATH=/share/apps/R/<newest version>/bin:$PATH

Running the Workflow

Workflow Configuration

Cluster Configuration

Disclaimer:

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