czid-cli

CZ ID CLI

This project is under active development and in its beta phase. It should be fairly stable but there may be some issues. If you experience an issue please let us know.

A Command Line Interface for CZ ID.

Rewrite of https://github.com/chanzuckerberg/idseq-cli.

Getting Started

Installation

Currently only binaries are available. More types of packages coming soon.

Linux

There are lots of options to install on Linux.

1. Download our latest .deb package.
2. (Alternatively) Download with curl: curl -L https://github.com/chanzuckerberg/czid-cli/releases/latest/download/czid-cli_linux_amd64.deb -o czid-cli_linux_amd64.deb
3. Install the package: sudo dpkg -i czid-cli_linux_amd64.deb
4. (Optional) Remove the package file rm czid-cli_linux_amd64.deb

1. Download our latest .rpm package
2. (Alternatively) Download with curl: curl -L https://github.com/chanzuckerberg/czid-cli/releases/latest/download/czid-cli_linux_amd64.rpm -o czid-cli_linux_amd64.rpm
3. Install the package: sudo rpm -i czid-cli_linux_amd64.rpm
4. (Optional) Remove the package file: rm czid-cli_linux_amd64.rpm

1. Make sure you have Homebrew for Linux
2. Add the chanzuckerberg tap: brew tap chanzuckerberg/tap
3. Install the package: brew install czid-cli

Follow the instructions for installing from binaries.

MacOs

czid-cli is available via homebrew and natively supports Apple Silicon! (via the darwin_arm64 binary)

1. Make sure you have Homebrew for Linux
2. Add the chanzuckerberg tap: brew tap chanzuckerberg/tap
3. Install the package: brew install czid-cli

Follow the instructions for installing from binaries.

Windows

Follow the instructions for installing from binaries.

From Binaries

1. Navigate to our latest release.

2. Available binaries will be under the Assets tab as archives (.tar.gz for Linux + MacOS, .zip for Windows)

3. Download appropriate archive for your operating system and architecture

4. Unzip the file, the czid executable will be inside

   Linux + MacOS: tar -xf path/to/archive.tar.gz

   Windows: expand-archive -path 'c:\path\to\archive.zip' -destinationpath '.\czid-cli'

5. Files with shell completions are also inside so you can move them to the appropriate place for your shell

6. To use the binary you either need to add it to your PATH so you can execute it as czid or execute the binary directly with the path to the binary (i.e. /path/to/czid on Linux + MacOS or C:\path\to\czid.exe on windows). If you are executing the binary using it's path keep in mind that you should use the path to the czid binary instead of the czid command every time you use it.

Note on MacOS: Currently we don't sign our binary so you will need to manually remove the quarentine attribute from the binary: sudo xattr -d com.apple.quarantine path/to/binary

Basic Usage

Setup

First log in with your CZ ID account:

czid login

You will be prompted to log in with your CZ ID account via the web.

Accept the user agreement:

czid accept-user-agreement

This will print the user agreement and prompt you for your agreement.

Upload a Single Sample

You can use the CZ ID CLI to upload samples to upload a single sample to CZ ID. You can upload a single file for single end reads or two files for paired end reads. Supported file types: .fastq/.fq/.fasta/.fa/.fastq.gz/.fq.gz/.fasta.gz/.fa.gz.

Optionally, you can create a metadata CSV file for your sample. You can skip this step and specify your metadata with command line flags. For instructions on creating this file see:

• Instructions: https://czid.org/metadata/instructions
• Metadata dictionary and supported host genomes: https://czid.org/metadata/dictionary
• Metadata CSV template: https://czid.org/metadata/metadata_template_csv

Be sure to set the sample name in the Sample Name column of the CSV to the same name you pass to the upload-sample command with -s/--sample-name. If you would like to specify your metadata entirely with -m flags you don't need to include a --metadata-csv. If you have specified all of your metadata in the metadata csv you don't need to include any -m flags. -m flags override metadata from the csv.

Once you have set up you can use the upload-sample command to upload your sample to CZ ID.

Illumina

Linux + MacOS:

czid metagenomics upload-sample \
  -p 'Project Name' \
  -s 'Sample Name' \
  --sequencing-platform Illumina \
  --metadata-csv your_metadata.csv \
  -m 'Metadata Name=Metadata Value' \
  your_sample_R1.fastq.gz your_sample_R2.fastq.gz

Windows:

czid metagenomics upload-sample `
  -p "Project Name" `
  -s "Sample Name" `
  --sequencing-platform Illumina `
  --metadata-csv your_metadata.csv `
  -m "Metadata Name=Metadata Value" `
  your_sample_R1.fastq.gz your_sample_R2.fastq.gz

Note: The sample name is optional. If it is not included it will be computed from your input file name based on the same rules as uploading multiple samples.

Nanopore

Linux + MacOS:

czid metagenomics upload-sample \
  --project 'Your Project ID' \
  --sample-name 'Your Sample Name' \
  --metadata-csv 'Your_metadata_file.csv' \
  --sequencing-platform 'Nanopore' \
  --guppy-basecaller-setting 'hac' \
  your_sample.fastq.gz

Windows:

czid metagenomics upload-sample `
  --project "Your Project ID" `
  --sample-name "Your Sample Name" `
  --metadata-csv "Your_metadata_file.csv" `
  --sequencing-platform "Nanopore" `
  --guppy-basecaller-setting "hac" `
  your_sample.fastq.gz

Upload Multiple Samples

The CZ ID CLI can search a directory for read files and upload supported files as samples. Supported file types are: .fastq/.fq/.fasta/.fa/.fastq.gz/.fq.gz/.fasta.gz/.fa.gz. Sample names are computed based on the names of the files. Sample names the base name of the file with the extension, _R1, _R2, _R1_001, and _R2_001 removed. If two files have the same sample name and one has R1 and the other has R2 the files will be uploaded to the same sample as paired reads. Since only the base name of the file and no parent directories are taken into account file names must be globally unique (except for the same sample's R1 and R2 files). Here are a few examples of sample names for various paths:

• your_directory_of_samples/my_sample.fasta => my_sample
• your_directory_of_samples/sample_one/sample_one_R1.fastq.gz => sample_one
• your_directory_of_samples/sample_one/sample_one_R2.fastq.gz => sample_one (pair of the above example)
• your_directory_of_samples/some_directory/some_other_directory/sample_two_R1_001.fa.gz => sample_two

This is the first pass of directory uploads and we would like to support more directory structures. If you have any suggestions for directory structure uploads we'd love to hear from you.

Optionally, you can create a metadata CSV file for your sample. You can skip this step and specify your metadata with command line flags. For instructions on creating this file see:

• Instructions: https://czid.org/metadata/instructions
• Metadata dictionary and supported host genomes: https://czid.org/metadata/dictionary
• Metadata CSV template: https://czid.org/metadata/metadata_template_csv

To associate a row of metadata with a sample you must enter the correct sample name in the Sample Name column of the CSV. If you would like to specify your metadata entirely with -m flags you don't need to include a --metadata-csv. If you have specified all of your metadata in the metadata csv you don't need to include any -m flags. -m flags override metadata from the csv.

Once you have set up you can use the upload-samples command to upload your directory to CZ ID.

Illumina

Linux + MacOS:

czid metagenomics upload-samples \
  -p 'Project Name' \
  --sequencing-platform Illumina \
  --metadata-csv your_metadata.csv \
  -m 'Metadata Name=Metadata Value' \
  your_directory_of_samples

Windows:

czid metagenomics upload-samples `
  -p "Project Name" `
  --sequencing-platform Illumina `
  --metadata-csv your_metadata.csv `
  -m "Metadata Name=Metadata Value" `
  your_directory_of_samples

Nanopore

Linux + MacOS:

czid metagenomics upload-samples \
  --project 'Your Project ID' \
  --metadata-csv 'Your_metadata_file.csv' \
  --sequencing-platform 'Nanopore' \
  --guppy-basecaller-setting 'hac' \
  your_directory_of_samples

Windows:

czid metagenomics upload-samples `
  --project "Your Project ID" `
  --metadata-csv "Your_metadata_file.csv" `
  --sequencing-platform "Nanopore" `
  --guppy-basecaller-setting "hac" `
  your_directory_of_samples

Configuration

czid-cli can be configured with environment variables or files. By default configurations are saved in your system's default configuration directory under a directory called czid-cli in a yml file called config.yml. You can specify a custom configuration file with the --config flag for any command. Some commands modify your configuration like accept-user-agreement. These will modify whatever configuration file you specify, or the default if none are specified. Every configuration can be set as an environment variable with the prefix CZID_CLI_. For example, the secret config can be set with the environment variable: CZID_CLI_SECRET.

Configuration Options

• secret: a secret used to persistently authenticate with CZ ID. Generated by running: czid login --persistent
• accepted_user_agreement: set to Y if the user has accepted the user agreement. Setting this manually means you accept the user agreement. Also set via: czid accept-user-agreement

Differences from version 1

• Resume uploads that have been interrupted
• Faster uploads (on systems with high bandwidth) due to multithreading
• Distributed as a single binary for easier installation that doesn't rely on dependencies on the user's machine
• Shell completion support
• Structured with commands and subcommands to make room for future functionality
• Log in in the web via your CZ ID account instead of using a static token
• Critical bugfixes
• Uploads without the need for user prompts
• Supports configuration files and environment variable configuration instead of relying solely on flags

Contributing

This project is not seeking contributions at this time. It is tighly coupled to the CZ ID Web App, it's features, it's APIs, and it's development goals. Please feel free to raise issues for feature requests or bugs.

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected].

Reporting Security Issues

Please note: If you believe you have found a security issue, please responsibly disclose by contacting us at [email protected].

See SECURITY.md for more information.