gpas 0.14.0

The command line interface for the GPAS

gpas-client

The command line and Python API client for the Global Pathogen Analysis Service. Enables secure sample upload with client-side human read removal and retrieval of analytical outputs.

Install

Installing Miniconda

If the conda package manager is already installed, skip this step, 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

• If your Mac has an Apple processor (M1/M2), first run the following command using Terminal:

  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 the GPAS CLI

• Only if using a Mac with an Apple processor (M1/M2), run the following command using Terminal:

  arch -x86_64 zsh
  

• Perform the installation:

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

• Test the installation:

  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 linking results later.

Downloading output files (gpas download)

Download output files associated with a one or more sample GUIDs, or a batch defined by the mapping CSV generated during upload. When a mapping CSV is used, files are prefixed with the sample names provided at upload, otherwise files are prefixed with the sample GUID.

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

# 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

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

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 -f environment-dev.yml
pip install --editable .

Updating

git pull origin main
gpas --version

Using a local development server

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

To unset:

unset GPAS_HOST
unset GPAS_PROTOCOL