gpas 0.18.0

The command line and Python client for the GPAS platform

GPAS CLI

The command line and Python API client for the GPAS mycobacterial platform. Enables secure sample upload with client-side human read removal and retrieval of analytical outputs.

Install

Installing Miniconda

If a conda package manager is already installed, skip to Installing the GPAS CLI, otherwise:

Linux

• In a terminal console, install Miniconda, following instructions and accepting default options:

  curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  bash Miniconda3-latest-Linux-x86_64.sh
  

MacOS

The GPAS CLI requires an x86_64 conda installation. If your Mac has an Apple processor, you must disable or delete any existing arm64 conda installations before continuing.

• If your Mac has an Apple processor, using Terminal, firstly run:

  arch -x86_64 zsh
  

• Install Miniconda using Terminal, following instructions and accepting default options:

  curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
  bash Miniconda3-latest-MacOSX-x86_64.sh
  

Installing or updating the GPAS CLI

• If using a Mac with an Apple processor, using Terminal, firstly run:

  arch -x86_64 zsh
  

• Perform the installation/upgrade:

  conda create --yes -n gpas -c conda-forge -c bioconda hostile
  conda activate gpas
  pip install gpas
  

• Test:

  gpas --version
  

Usage

Ensure that the conda environment is active:

conda activate gpas

Help

Run gpas --help for an overview of CLI subcommands. For help with a specific subcommand, use e.g. gpas auth --help

Authentication (gpas auth)

The first time you use the CLI, you will need to authenticate by running gpas auth and entering your username and password. This token will be used automatically for subsequent commands.

gpas auth
Enter your username: [e-mail]
Enter your password: ***************

Uploading samples (gpas upload)

Performs metadata validation and client-side removal of human reads in each of your samples before uploading sequences to the GPAS platform.

gpas upload tests/data/illumina.csv

This generates a mapping CSV (e.g. a5w2e8.mapping.csv) linking your local sample names with their randomly generated remote identifiers (GUIDs). Keep this file safe as it's useful for downloading and relinking results later.

Downloading files (gpas download)

Downloads the output (and/or input) files associated with a batch of samples given a mapping CSV generated during upload, or one or more sample GUIDs. When a mapping CSV is used, by default downloaded file names are prefixed with the sample names provided at upload. Otherwise downloaded files are prefixed with the sample GUID.

# Download the main reports for all samples in a5w2e8.mapping.csv
gpas download a5w2e8.mapping.csv

# Download the main and speciation reports for samples in a5w2e8.mapping.csv
gpas download a5w2e8.mapping.csv --filenames main_report.json,speciation_report.json

# Download the main report for one sample
gpas download 3bf7d6f9-c883-4273-adc0-93bb96a499f6

# Download the main report for two samples
gpas download 3bf7d6f9-c883-4273-adc0-93bb96a499f6,6f004868-096b-4587-9d50-b13e09d01882

# Save downloaded files to a specific directory
gpas download a5w2e8.mapping.csv --out-dir results

# Download input files
gpas download --inputs a5w2e8.mapping.csv --filenames ""

Querying sample metadata (gpas query)

Fetches either the processing status (gpas query status) or raw metadata (gpas query raw) of one more samples given a mapping CSV generated during upload, or one or more sample GUIDs.

# Query the processing status of all samples in a5w2e8.mapping.csv
gpas query status a5w2e8.mapping.csv

# Query the processing status of a single sample
gpas query status 3bf7d6f9-c883-4273-adc0-93bb96a499f6

# Query all available metadata in JSON format
gpas query raw a5w2e8.mapping.csv

Support

For technical support, please open an issue or contact [e-mail]

Development

Development install

git clone https://github.com/GlobalPathogenAnalysisService/cli.git
cd cli
conda env create -y -f environment-dev.yml
pip install --editable .

Updating

git pull origin main
gpas --version

Using alternate API servers

export GPAS_HOST="dev.portal.gpas.world"

To unset

unset GPAS_HOST

Using a local development server

export GPAS_HOST="localhost:8000"
export GPAS_PROTOCOL="http"

To unset:

unset GPAS_HOST
unset GPAS_PROTOCOL

Releasing a new version

pytest
# Increment version string inside src/gpas/__init__.py
git tag 0.xx.0  # Tag new version
git push origin main --tags  # Push including tags
flit build
flit publish  # Uploads to PyPI given appropriate permission
# Announce in Slack CLI channel
# PR gpas/gpas/settings.py with new version