Quick Start#

Get up and running with your first workflow in Python.#

In this quickstart, you install the Latch SDK and register a workflow to sort and assemble COVID genomes. The workflow makes use of two computational tools, SAM tools and bowtie, which will allow us to reconstruct the COVID genome from its reads.


Step 1: Set up your developer environment#

For Linux/ MacOS#

We recommend installing Latch SDK in a fresh environment for best behaviour. To do so, you can use venv.

python3 -m venv env
source env/bin/activate

For Windows#

The Latch SDK is a Python package, so we recommend installing Latch SDK in a fresh environment for best behavior. To do so, you can use venv.

  1. First, install the WSL command:

wsl --install

This command will enable the features necessary to run WSL and install the Ubuntu distribution of Linux.

  1. Activate the Linux shell:


Now, you are in a Linux environment and can create a virtual environment like so:

python3 -m venv env
source env/bin/activate

Using Conda#

Alternatively, you can use conda to create your environment:

conda create --name latch python==3.10

Step 2: Install Latch#

The Latch SDK is available as a Python package.

Latch currently supports Python >=3.8, <3.11.

Install it using pip:

python3 -m pip install latch

Step 3: Initialize Workflow Directory#

Bootstrap a new workflow directory by running latch init from the command line:

latch init covid-wf

The command opens a list of workflow templates that you can select from. for this tutorial, select Subprocess Example:

Workflow templates

The command creates a folder in your current working directory called covid-wf. Inside that folder, it will generate the initial project structure:

├── README.md
├── bowtie2
│   ├── bowtie2
│   └── ...
├── reference
│   ├── wuhan.1.bt2
│   └── ...
├── system-requirements.txt
├── version
└── wf
    ├── __init__.py
    ├── assemble.py
    └── sort.py

Step 4: Register your first workflow#

To get a live version of your workflow on Latch, simply type:

latch register --remote --yes covid-wf

When registering the workflow for the first time, you will be prompted to log into Latch via the browser.

Optional: Registering workflow on a machine without a browser#

If you are using a virtual machine without a browser, you will be prompted to enter an API key. To retrieve your key:

  • Navigate to your Personal Workspace. personal workspace

  • Visit the Developer Settings > Access Tokens API key for Latch CLI

  • Copy the API key, and paste to the terminal prompt

Once registration completes, visit Latch Console, and you will see a live, no-code interface of your assemble and sort workflow!

Interface UI

Step 5: Running your workflow on Latch#

To launch your first workflow, make sure that you are on your workflow page in Latch Console. Then, select the Test Data and click Launch.

Once the workflow finishes running, you can see both the covid_assembly.sam and covid_sorted.bam files on Latch Console. The SAM file contains the sequence alignment data, and the BAM file is the binary version of the SAM file.

To further check that the genome is aligned properly, simply double click on the output file to open an IGV.

Inputs UI

The next time your scientists want to reconstruct COVID genome from sequencing reads, they can visit your workflow on Latch Console!

Next Steps#