installation with conda

[stephenturner]

On https://dahak-metagenomics.github.io/dahak/installing/, might be useful to add installation instructions using conda. Here's an environment i'm building so far (includes some things i need for simulation).

name: dahak
channels:
    - bioconda
    - conda-forge
    - defaults
dependencies:
    - art
    - nanosim
    - pbsim
    - singularity
    - snakemake
    - osfclient

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

conda env create -f dahak-conda-environment.yml

[stephenturner]

osfclient is also available on conda-forge installable via conda

[charlesreid1]

Just a note on the OSF client. We are downloading data from OSF using direct URLs. The last time I checked, the quay.io container for OSF client was marked with over 100 security vulnerabilities, around 40 of which were marked "serious". Plus it's not necessary to use to download data.

[charlesreid1]

I've added installation instructions for conda for non-pyenv users. I am going to leave out most of the environment.yml details, since dahak is using singularity and really shouldn't need to install things explicitly with conda, except installing snakemake. Let me know if this is more along the lines of what you were thinking.

Link to new section: https://dahak-metagenomics.github.io/dahak/installing/#installing-conda-with-python