Welcome to Gencove’s CLI documentation!

Indices and tables

Python library which enables you to use Gencoves’ research backend.

Supported Python versions are 2.7+ and 3.7+.

Quickstart

Installation

To check your default Python version, open an interactive shell and run:

python --version

To check if you have Python 3, open an interactive shell and run:

python3 --version

To install Gencove CLI Tool, open an interactive shell and run:

python<version> -m pip install gencove

If you want Gencove CLI Tool to be installed for your default Python installation, you can instead use:

python -m pip install gencove

Using Gencove CLI Tool

To start using Gencove CLI Tool, open an interactive shell and run:

gencove --help

This will output all available commands.

gencove

Gencove’s command line interface.

gencove [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

upload

Upload FASTQ files to Gencove’s system.

param source:folder that contains fastq files to be uploaded.
type source:.fastq.gz, .fastq.bgz, .fq.gz, .fq.bgz
param destination:
 (optional) ‘gncv://’ notated folder on Gencove’s system, where the files will be uploaded to.
type destination:
 str
Example:
gencove sync test_dataset gncv://test
gencove upload [OPTIONS] SOURCE [DESTINATION]

Options

--host <host>

Optional Gencove API host, including http/s protocol. Defaults to https://api.gencove.com

--email <email>

Gencove user email to be used in login. Can be passed as GENCOVE_EMAIL environment variable

--password <password>

Gencove user password to be used in login. Can be passed as GENCOVE_PASSWORD environment variable

Arguments

SOURCE

Required argument

DESTINATION

Optional argument

download

Download deliverables of a project.

Must specify either project id or sample ids.

param destination:
 path/to/save/deliverables/to.
type destination:
 str
param project_id:
 project id in Gencove’s system.
type project_id:
 str
param sample_ids:
 specific samples for which to download the results.

if not specified, download deliverables for all samples. :type sample_ids: list(str) :param file_types: specific deliverables to download results for. if not specified, all file types will be downloaded. :type file_types: list(str) :param skip_existing: skip downloading existing files :type skip_existing: bool

Examples:

Download all samples results:

gencove download ./results –project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db

Download some samples:

gencove download ./results –sample-ids 59f5c1fd-cce0-4c4c-90e2-0b6c6c525d71,7edee497-12b5-4a1d-951f-34dc8dce1c1d

Download specific deliverables:

gencove download ./results –project-id d9eaa54b-aaac-4b85-92b0-0b564be6d7db –file-types alignment-bam,impute-vcf,fastq-r1,fastq-r2

gencove download [OPTIONS] DESTINATION

Options

--project-id <project_id>

Gencove project ID

--sample-ids <sample_ids>

A comma separated list of sample ids for which to download the deliverables

--file-types <file_types>

A comma separated list of deliverable file types to download.

--host <host>

Optional Gencove API host, including http/s protocol. Defaults to https://api.gencove.com

--email <email>

Gencove user email to be used in login. Can be passed as GENCOVE_EMAIL environment variable

--password <password>

Gencove user password to be used in login. Can be passed as GENCOVE_PASSWORD environment variable

--skip-existing, --no-skip-existing

Skip downloading files that already exist in DESTINATION

Arguments

DESTINATION

Required argument