Project Templates Installation

Project Templates with Python virtual environment

Install Cookiecutter and other basic Python packages using the requirements.txt file.

localhost:~> virtualenv venv-templates
localhost:~> source venv-templates/bin/activate
localhost:~> pip install -r https://raw.githubusercontent.com/ncbi/pm4ngs/master/requirements.txt

Project Templates with Conda/BioConda

Conda should be already installed and configured.

localhost:~> wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
localhost:~> sh Miniconda3-latest-MacOSX-x86_64.sh

A Conda virtual environment will be created with name templates using these instructions:

localhost:~> wget https://raw.githubusercontent.com/ncbi/pm4ngs/master/conda-requirements.yaml
localhost:~> conda env create -f conda-requirements.yaml

If Conda is installed with prefix /gfs/conda you should see the available environments like in this block:

localhost:~> conda env list
# conda environments:
#
base                     /gfs/conda
templates             *  /gfs/conda/envs/templates

localhost:~>

To activate the templates env

localhost:~> conda activate templates
localhost:~>

Using the Template Project

This project template uses the workflow defined in the project cwl-ngs-workflows-cbb. Depending on the execution environment selected: docker, conda or programs in the path the project template will check the availability of the Bioinformatic tools required by the workflow.