README.md

ProteomX_Docker

ProteomX

Prerequisites & Sample run

ProteomX is provided as a stand-alone application as well as a set of docker images.

Docker based install

The docker image is defined in the main Dockerfile.

1. Ensure that docker is installed on your host machine (docker ps)
2. Go to architecture folder of your host machine (cd Amd64|cd Arm64)
3. ./scripts/retrieve_test_dataset.sh to pull sample datafiles from the CBIB servers
4. From the corresponding architecture directory, make image will build the ProteomX main image
5. Once the image is built :
   1. make shell will open a bash shell in a new container, in this container you can :
      1. /scripts/retrieve_test_dataset_docker.sh to pull sample datafiles from the CBIB servers
      2. /scripts/analyse_test_dataset_docker.sh to run a sample analysis pipeline on the test dataset. Results are available in the data/ExampleProject folder.
   2. make tests will run all unit tests
   3. make run project=PROJECTNAME will run all steps of the proteomX pipeline (e.g make run project=ExampleProject)
6. The container shares the following volumes with the host machine :
   1. data -> /data/ where all datasets and results are stored
   2. config_files -> /config_files where all job configurations are stored
   3. scripts -> /scripts/ where helper maintenance scripts are stored
   4. backend -> /backend/ where the (python) backend code is stored

Conda based install

1. Ensure that conda is installed on your host machine (conda info)
2. Ensure that R is installed on your host machine (R --version)
3. ./scripts/retrieve_test_dataset.sh to pull sample datafiles from the CBIB servers
4. Once the installation is complete :
   1. Run ./scripts/setup.sh
      1. to ensure repository integrity
      2. to install conda Proteomix environment if missing
      3. to install R packages if missing sample datafiles from the CBIB servers
   2. ./scripts/Conda_run.sh -i PROJECTNAME will run all steps of the proteomX pipeline (e.g ./scripts/Conda_run.sh -i ExampleProject)