test
Install conda/mamba
Option 1: install conda and then use it to install mamba
Follow the instructions here: https://docs.conda.io/projects/conda/en/stable/user-guide/install/linux.html
You can use wget
to download the miniconda installer.
Press q
to get through the terms of service.
At the end of installation, you will be asked:
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
You can say yes
, but you still need to restart the shell after:
==> For changes to take effect, close and re-open your current shell. <==
You could log out of the server and log back in, but a quicker way is to do:
source ~/.bashrc
If you don’t want conda to activate automatically every time you login, run
conda config --set auto_activate_base false
Now, ensuring that you have the base
conda environment open, run
https://mamba.readthedocs.io/en/latest/installation.html
to install mamba, which is just a faster version of conda (as in the first version of this site: https://mamba.readthedocs.io/en/latest/installation.html ).
Now, when we follow the instructions for the UM pipeline, we will use mamba
whenever they use conda
and it will run much faster.
Option 2: directly install mamba
TODO. It is potentially better to directly insteall mamba than to install it through conda.
Set up and run UM pipeline
Now, go to the UM pipeline page: https://github.com/goodest-goodlab/UM-CoV-Seq. Clone the repo as they say. Make sure conda
is activated.
We would like to load their pre-defined environment, but we use mamba
instead of conda.
So we run
mamba env create --file envs/UM-CoV-Seq.yml
You can then activate the environment just as they do:
conda activate UM-CoV-Seq
Next, follow the instructions to get the nextclade resources. We’ll call the directory nextclade-resources
, so you can run
nextclade dataset get --name sars-cov-2 --output-dir nextclade-resources
Copy the shared config file:
TODO
At this point, snakemake
has a bug, so run
mamba install 'tabulate=0.8.10'
Similarly, one of the packages uses an old version of numpy, so run
mamba install `numpy<1.24`
Similarly, we should use an older version of nextclade
, so run
mamba install -c bioconda 'nextclade=1.10'
We also need ggplot2
, ggrepl
, dplyr
:
mamba install -c conda-forge r-ggplot2
mamba install -c bioconda r-ggrepel
mamba install -c conda-forge r-dplyr
mamba install -c conda-forge r-stringr
mamba install -c conda-forge r-tidyr
Now, run the pipeline with
snakemake -s pipe_reads_to_lineages.smk --configfile config_files/my_config.yaml --dry-run
If that works, then run
snakemake -s pipe_reads_to_lineages.smk --configfile /home/shared_files/example_UM_config.yaml --cores 1
If you want to copy the results to your local machine, run