Team Project Template

This repository serves as the default template for analysis projects within the team.

Main Features

Buildable Package: This template can be built into a package and easily imported into other projects.

Modules Included: Comes with several built-in modules such as datatracker, teamconnector, and findhere to streamline your project development.

Use this template to jump-start your analysis projects and ensure you have a consistent structure across the team.

Installation

To get started with this template, follow these steps:

Create a new repository on GitHub by clicking "New" on the dashboard.

Choose a pre-defined template from the list under "Repository template."

Name your repository and set its visibility.

Click "Create repository" to initialize the repo with the chosen template.

Clone the repository to your local machine using the command git clone <your-new-repo-url>.

Make changes to the code as needed.

Push your changes to the repository using the command git push.

To customize this template for your project, you'll need to replace some placeholders:

Search for {{ cookiecutter.full_name }} and replace it with the appropriate full name associated with this repository.

Look for {{ cookiecutter.project_slug }} and substitute it with the repository name or slug you're using.

Replace {{ cookiecutter.project_short_description }} with a concise description of this repository's purpose or functionality.

Usage

Update pip

Update your pip package manager with the following command:

make update-pip

Create Environment

To create a new environment:

make create-env

After that, enter the created Conda environment and only run commands in that environment.

make act

Set Environment Variables

Make sure your environment variables are set appropriately according to teamconnector in ~/.env. To set up your environment variables:

make set-env
tcinit ~

Install Versioneer

To install Versioneer:

make install-version

Install Current Package

For an interactive installation of the current package:

make install

Update packages

Running make install will not install the most up-to-date packages from PyPI. To update all packages in requirements.txt to the newest version, you can use the following command:

make install-reqs

Manage Dependencies

To install or update the required packages:

make install-reqs
make install-dev

Version Information

Get Version

To get the version of this library:

make version

Get Specific Library Version

To get the version of a specific Python library (e.g., hail):

make lib-version NAME=hail
make hail-version

Install Java 11 using Conda Forge

Hail requires Java 11 for running on local machines, whether it's a SLURM cluster or a local Mac. You can use the Conda Forge package manager.

1. Open Terminal

2. Add Conda-Forge Channel

   conda config --add channels conda-forge

3. Install Java 11

   conda install -c conda-forge openjdk=11

4. Verify Installation

   java -version

Cite

Maintainer

TJ Singh lab @ singhlab@nygenome.org

Acknowledgements

Release Notes