cov-support

Install cov-support

1. Clone this repository and cd cov-support
2. conda env create -f environment.yml
3. conda activate cov-support
4. python setup.py install or pip install .

Note: we recommend using cov-support in the conda environment specified in the environment.yml file as per the instructions above. If you can't use conda for some reason, dependency details can be found in the environment.yml file.

Check the install worked

Type (in the cov-support environment):

cov-support

and you should see the help for cov-support printed.

Updating cov-support

To update:

1. conda activate cov-support
2. git pull
   pulls the latest changes from github
3. python setup.py install
   re-installs cov-support
4. conda env update -f environment.yml
   updates the conda environment

Update website

cov-support --update-web \
    --website-dir cov-lineages \
    --assignment-dir assignment \
    -d pangoLEARN/pangoLEARN/data \
    --updated-metadata data-dir/metadata.csv \
    --lineage-descriptions pangoLEARN/pangoLEARN/supporting_information/lineage_notes.txt

Make guide tree and alignment

cov-support --pangolin-prep \
    -d data_dir \
    --num-taxa 5 

Full usage

usage: cov-support [-h] [-o OUTDIR] [-d DATA] [--pangolin-prep]
                   [--num-taxa NUM_TAXA] [--update-web]
                   [--website-dir WEBSITE_DIR]
                   [--assignment-dir ASSIGNMENT_DIR]
                   [--updated-metadata METADATA]
                   [--lineage-descriptions DESCRIPTIONS] [-n] [-t THREADS]
                   [--verbose] [-v]

cov-support: update guide tree or train a new model. Update webpages. Do all
sorts of cov-lineage-support-related tasks

optional arguments:
  -h, --help            show this help message and exit
  -o OUTDIR, --outdir OUTDIR
                        Output directory. Default: current working directory
  -d DATA, --data DATA  Data directory minimally containing alignment.fasta,
                        global.tree metadata.csv and lineages.csv
  --pangolin-prep       Run legacy pangolin prep pipeline
  --num-taxa NUM_TAXA   Number of taxa in guide tree
  --update-web          Run website update pipeline
  --website-dir WEBSITE_DIR
                        Path to website repo
  --assignment-dir ASSIGNMENT_DIR
                        Path to assignment repo
  --updated-metadata METADATA
                        Updated metadata file
  --lineage-descriptions DESCRIPTIONS
                        Updated descriptions file
  -n, --dry-run         Go through the motions but don't actually run
  -t THREADS, --threads THREADS
                        Number of threads
  --verbose             Print lots of stuff to screen
  -v, --version         show program's version number and exit