initial conda-env requirements for data_buddy

[russHyde]

Need a requirements.txt / environment.yml for creating a minimal conda env that will allow the sidekick setup program, setup-scripts and Snakefiles

[russHyde]

Required as of 2019-04-10:

• pip
• snakemake [suggest >=5.3]
• Rscript (if including an R environment) [>=3.4.1]
• sh

[russHyde]

Suggest:

channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - snakemake >=5.3
  { % how do you specify conditional dependencies : cookiecutter.is_r_required %}
  - r-base >= 3.4.1
  { % how do you terminate a conditional dependency? % }
  - pip
  - sh

[russHyde]

When an R package is to be produced (either a local, or installation of a cloned / copied one), we also require:

• r-desc
• r-devtools

[russHyde]

Suggest just printing a message & exiting.

If conda isn't even available

# Environment manager `conda` is a prerequisite for setting-up  and running this project
# - please install `conda` using `miniconda` or `anaconda`

If the computer has an environment of the correct name, but it hasn't been activated

# Environment `env_name` detected
# Environment `env_name` has not been activated
# - please rerun this project after activating `env_name`
conda activate <env_name>

If the computer contains an environment of the correct name, but it doesn't contain the requirements:

# Environment `env_name` detected
# Environment `env_name` does not contain all requirements for setting-up this project
# - please install using:
conda install --name <env_name> -c conda-forge -c bioconda snakemake pip sh 
conda install --name <env_name> -c conda-forge -c bioconda r-base r-desc r-devtools

If the computer does not contain an environment of the correct name:

# Environment `env_name` not detected
# Please install using:
conda create --name <env_name>
conda install --name <env_name> -c conda-forge -c bioconda snakemake pip sh
conda install --name <env_name> -c conda-forge -c bioconda r-base r-desc r-devtools