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Installation
In order to install conda, please follow the guide lines described on the official Conda web-page.
This will likely be:
# Conda pre-requisites
apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
# Download latest conda installer
wget https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh
# Run the installer
bash ~/Downloads/Anaconda3-2019.03-Linux-x86_64.sh
You can alternatively try the script: setup.sh within the .circleci directory, by typing bash .circleci/setup.sh. But remember, this is provided for machine without either conda, nor miniconda installed.
The next step to use this workflow is to clone it to your computer. This can be easily done with git (which you have installed in your virtual environment few seconds ago!
Here we go:
git clone https://github.com/tdayris-perso/vcf-annotate-snpeff-snpsift.git
We are going to use Python 3.7. No other options. Forget about python 2.7, it will be dropped out of support before 2020'. In vcf-annotate-snpeff-snpsift, we use formatted strings available at python 3.6. It is not excluded that further development will include python 3.7 exclusive behaviors. Go for latest python !
A yaml description of all dependencies is embedded with this work flow under envs/workflow.yaml. Install all dependencies with:
make conda-install
In which python, datrie, snakemake, pandas and git are non-optional and essential. Pytest, is used to perform unit-testing. pbgzip is used to archive the completed work. Finally, jinja2, pygraphviz, flask, openssl, zlib, and networkx are here to handle dynamic snakemake's reporting.
Every single time you will use this pipeline, you have to activate that conda environment. The activation command will not be repeated everywhere in this wiki, so please, don't forget it!
To activate the environment, use:
conda activate vcf-annotate-snpeff-snpsift
Typos corrections and issues are welcomed