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README.md

GitHub release (latest SemVer) Snakemake Documentation Status tests Contributor Covenant

RAPIDS

Reproducible Analysis Pipeline for Data Streams

For more information refer to our documentation

By MoSHI, University of Pittsburgh

Installation

For RAPIDS installation refer to to the documentation

For the installation of the Docker version

  1. Follow the instructions to setup RAPIDS via Docker (from scratch).

  2. Delete current contents in /rapids/ folder when in a container session.

    cd ..
    rm -rf rapids/{*,.*}
    cd rapids
    
  3. Clone RAPIDS workspace from Git and checkout a specific branch.

    git clone "https://repo.ijs.si/junoslukan/rapids.git" .
    git checkout <branch_name>
    
  4. Install missing “libpq-dev” dependency with bash.

    apt-get update -y
    apt-get install -y libpq-dev
    
  5. Restore R venv. Type R to go to the interactive R session and then:

    renv::restore()
    
  6. Install cr-features module From: https://repo.ijs.si/matjazbostic/calculatingfeatures.git -> branch modifications_for_rapids. Then follow the "cr-features module" section below.

  7. Install all required packages from environment.yml, prune also deletes conda packages not present in environment file.

    conda env update --file environment.yml –prune
    
  8. If you wish to update your R or Python venvs.

    R in interactive session:
    renv::snapshot()
    Python: 
    conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' | sed 's/^.*mkl=.*$/  - mkl/' >  environment.yml
    

cr-features module

This RAPIDS extension uses cr-features library accessible here.

To use cr-features library:

  • Follow the installation instructions in the README.md.

  • Copy built calculatingfeatures folder into the RAPIDS workspace.

  • Install the cr-features package by:

    pip install path/to/the/calculatingfeatures/folder
    e.g. pip install ./calculatingfeatures if the folder is copied to main parent directory
    cr-features package has to be built and installed everytime to get the newest version. 
    Or an the newest version of the docker image must be used.