# Cancer Invasion Workflow ## Table of Contents - [Cancer Invasion Workflow](#cancer-invasion-workflow) - [Table of Contents](#table-of-contents) - [Description](#description) - [Contents](#contents) - [Building Blocks](#building-blocks) - [Workflows](#workflows) - [Resources](#resources) - [Tests](#tests) - [Instructions](#instructions) - [Local machine](#local-machine) - [Requirements](#requirements) - [Usage steps](#usage-steps) - [MareNostrum 4](#marenostrum-4) - [Requirements in MN4](#requirements-in-mn4) - [Usage steps in MN4](#usage-steps-in-mn4) - [Mahti or Puhti](#mahti-or-puhti) - [Requirements](#requirements) - [Steps](#steps) - [License](#license) - [Contact](#contact) ## Description Uses multiscale simulations to describe cancer progression into invasion. The workflow uses the following building blocks, described in order of execution: 1. PhysiBoSS-Invasion For details on individual workflow steps, see the user documentation for each building block. [`GitHub repository`]() ## Contents ### Building Blocks The ``BuildingBlocks`` folder contains the script to install the Building Blocks used in the Cancer Invasion Workflow. ### Workflows The ``Workflow`` folder contains the workflows implementations. Currently contains the implementation using PyCOMPSs and Snakemake (in progress). ### Resources The ``Resources`` folder contains dataset files. ### Tests The ``Tests`` folder contains the scripts that run each Building Block used in the workflow for the given small dataset. They can be executed individually for testing purposes. ## Instructions ### Local machine This section explains the requirements and usage for the Cancer Invasion Workflow in a laptop or desktop computer. #### Requirements - [`permedcoe`](https://github.com/PerMedCoE/permedcoe) package - [PyCOMPSs](https://pycompss.readthedocs.io/en/stable/Sections/00_Quickstart.html) / [Snakemake](https://snakemake.readthedocs.io/en/stable/) - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) #### Usage steps 1. Clone this repository: ```bash git clone https://github.com/PerMedCoE/cancer-invasion-workflow ``` 2. Install the Building Blocks required for the Cancer Invasion Workflow: ```bash cancer-invasion-workflow/BuildingBlocks/./install_BBs.sh ``` 3. Get the required Building Block images from the project [B2DROP](https://b2drop.bsc.es/index.php/f/444350): - Required images: - PhysiCell-Invasion.singularity The path where these files are stored **MUST be exported in the `PERMEDCOE_IMAGES`** environment variable. > :warning: **TIP**: These containers can be built manually as follows (be patient since some of them may take some time): 1. Clone the `BuildingBlocks` repository ```bash git clone https://github.com/PerMedCoE/BuildingBlocks.git ``` 2. Build the required Building Block images ```bash cd BuildingBlocks/Resources/images sudo singularity build PhysiCell-Invasion.sif PhysiCell-Invasion.singularity cd ../../.. ``` **If using PyCOMPSs in local PC** (make sure that PyCOMPSs in installed): 4. Go to `Workflow/PyCOMPSs` folder ```bash cd Workflows/PyCOMPSs ``` 5. Execute `./run.sh` **If using Snakemake in local PC** (make sure that SnakeMake is installed): 4. Go to `Workflow/SnakeMake` folder ```bash cd Workflows/SnakeMake ``` 5. Execute `./run.sh` > **TIP**: If you want to run the workflow with a different dataset, please update the `run.sh` script setting the `dataset` variable to the new dataset folder and their file names. ### MareNostrum 4 This section explains the requirements and usage for the Cancer Invasion Workflow in the MareNostrum 4 supercomputer. #### Requirements in MN4 - Access to MN4 All Building Blocks are already installed in MN4, and the Cancer Invasion Workflow available. #### Usage steps in MN4 1. Load the `COMPSs`, `Singularity` and `permedcoe` modules ```bash export COMPSS_PYTHON_VERSION=3 module load COMPSs/3.1 module load singularity/3.5.2 module use /apps/modules/modulefiles/tools/COMPSs/libraries module load permedcoe ``` > **TIP**: Include the loading into your `${HOME}/.bashrc` file to load it automatically on the session start. This commands will load COMPSs and the permedcoe package which provides all necessary dependencies, as well as the path to the singularity container images (`PERMEDCOE_IMAGES` environment variable) and testing dataset (`CANCERINVASIONWORKFLOW_DATASET` environment variable). 2. Get a copy of the pilot workflow into your desired folder ```bash mkdir desired_folder cd desired_folder get_cancerinvasionworkflow ``` 3. Go to `Workflow/PyCOMPSs` folder ```bash cd Workflow/PyCOMPSs ``` 4. Execute `./launch.sh` This command will launch a job into the job queuing system (SLURM) requesting 2 nodes (one node acting half master and half worker, and other full worker node) for 20 minutes, and is prepared to use the singularity images that are already deployed in MN4 (located into the `PERMEDCOE_IMAGES` environment variable). It uses the dataset located into `../../Resources/data` folder. > :warning: **TIP**: If you want to run the workflow with a different dataset, please edit the `launch.sh` script and define the appropriate dataset path. After the execution, a `results` folder will be available with with Cancer Invasion Workflow results. ### Mahti or Puhti This section explains how to run the Cancer Invasion workflow on CSC supercomputers using SnakeMake. #### Requirements - Install snakemake (or check if there is a version installed using `module spider snakemake`) - Install workflow, using the same steps as for the local machine. With the exception that containers have to be built elsewhere. #### Steps 1. Go to `Workflow/SnakeMake` folder ```bash cd Workflow/SnakeMake ``` 2. Edit `launch.sh` with the correct partition, account, and resource specifications. 3. Execute `./launch.sh` > :warning: Snakemake provides a `--cluster` flag, but this functionality should be avoided as it's really not suited for HPC systems. ## License [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0) ## Contact This software has been developed for the [PerMedCoE project](https://permedcoe.eu/), funded by the European Commission (EU H2020 [951773](https://cordis.europa.eu/project/id/951773)). 