Installation via conda (different ways) failed

[ravinkazo]

Hello everyone,

Hope you are all well.
I need your help please...

I tried installing Artic pipeline in different ways, but they all failed.

Initially I tried the following, as per https://artic.network/ncov-2019/ncov2019-it-setup.html:

conda env create -f artic-ncov2019/environment.yml

But I got this error:
Error: Could not locate 'conda-env'

I also tried other ways:
conda install -c bioconda artic

It gave me this error:

Fetching package metadata: ...Could not connect to https://conda.binstar.org/bioconda/linux-64/
Error: No packages found matching: artic

Also:
conda install -c conda-forge artic

Unfortunately, same results:

Fetching package metadata: ...Could not connect to https://conda.binstar.org/conda-forge/linux-64/
Error: No packages found matching: artic

Thank you in advance for your time and help.

[koppk]

Hi ravinkazo,

you might try via mamba (often faster than conda).

But first you must install conda.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sudo chmod 755 Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
source .bashrc

conda config --set auto_activate_base false

conda install -n base -c conda-forge mamba --yes

mamba create -n artic-ncov2019 -c conda-forge -c bioconda -c defaults artic artic-network::rampart snakemake-minimal --yes

conda activate artic-ncov2019