Installation
Installation instructuons for both the ARTIC analysis pipeline, as well as RAMPART for real-time monitoring.
Linux
miniconda
Visit https://docs.conda.io/en/latest/miniconda.html and download the appropriate binary. Most likely that will be the following:
Python 3.8 Miniconda3 Linux 64-bit
Command line download:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Output example:
--YYYY-MM-DD HH:MM:SS-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)... xxx.xxx.xxx.x, xxx.xxx.xxx.x, yyyy:yyyy::yyyy:yyyy, ...
Connecting to repo.anaconda.com (repo.anaconda.com)|xxx.xxx.xxx.x|:xxx... connected.
HTTP request sent, awaiting response... 200 OK
Length: 94235922 (90M) [application/x-sh]
Saving to: 'Miniconda3-latest-Linux-x86_64.sh’
Miniconda3-latest-L 100%[===================>] 89.87M 5.41MB/s in 17s
YYYY-MM-DD HH:MM:SS (5.36 MB/s) - 'Miniconda3-latest-Linux-x86_64.sh’ saved [94235922/94235922]
Modify the shell file with execute permissions
chmod +x Miniconda3-latest-Linux-x86_64.sh
run the shell file
./Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 py38_4.9.2
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
Press ENTER
The Lisence information will apper. Press SPACE multiple times to scroll to the bottom.
insert lisence image
Last updated September 28, 2020
Do you accept the license terms? [yes|no]
[no] >>>
type yes and hit ENTER
Do you accept the license terms? [yes|no]
[no] >>> yes
Miniconda3 will now be installed into this location:
/home/jamfer/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/jamfer/miniconda3] >>>
either hit enter to install to the default /HOME/USER/miniconda3 folder, or enter your own directory. For example, enter ./miniconda3 to build in the current directory
...
six pkgs/main/linux-64::six-1.15.0-py38h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0
wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>>
type yes and enter (we will fix the problems this causes in a moment)
...
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
./Miniconda3-latest-Linux-x86_64.sh: 494: ./Miniconda3-latest-Linux-x86_64.sh: [[: not found
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/condabin/conda
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/bin/conda
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/bin/conda-env
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/bin/activate
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/bin/deactivate
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/etc/profile.d/conda.sh
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/etc/fish/conf.d/conda.fish
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/shell/condabin/Conda.psm1
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/shell/condabin/conda-hook.ps1
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change /home/jamfer/data/SARS-CoV-2/docs/miniconda3/etc/profile.d/conda.csh
modified /home/jamfer/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
Close terminal and open again
which conda
mine says
/home/jamfer/data/SARS-CoV-2/docs/miniconda3/condabin/conda
which is where I just installed it.
We now need to remove the automatic conda init from ~/.bashrc so it does not interfere with other environments.
open the ~/.bashrc file and find the conda init commands
cat ~/.bashrc
...
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/jamfer/data/SARS-CoV-2/docs/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/home/jamfer/data/SARS-CoV-2/docs/miniconda3/etc/profile.d/conda.sh" ]; then
. "/home/jamfer/data/SARS-CoV-2/docs/miniconda3/etc/profile.d/conda.sh"
else
export PATH="/home/jamfer/data/SARS-CoV-2/docs/miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
Yours will look slightly different due to different paths.
We need to copy this information into a separate shell file, then remove this from ~/.bashrc .
copy everything similar to above
then copy into a file called something like ~/conda_init.sh
and remove the same section from ~/.bashrc
Close and open terminal again
To activate conda, we can now run
source ~/conda_init.sh
ARTIC and RAMPART
Download the repo from github
cd
git clone https://github.com/artic-network/artic-ncov2019.git
cd artic-ncov2019
conda env remove -n artic-ncov2019
conda env create -f environment.yml
insert image of venv installing
Other Operating Systems will work, but may need system specific changes to installation method. Let us know if you would like this extended to other Operating Systems.