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.