Quick Start Guide¶

To get started with CALYPR, you will need to install git-lfs and git-drs, a "git" like command line tool for uploading and downloading files to the gen3 platform.

Git-LFS Installation Instructions¶

To use CALYPR, you must first install Git Large File Storage (LFS) on your system. This allows Git to efficiently handle the large genomic data files.

macOSLinuxWindows

Install using Homebrew

brew install git-lfs

Install via Package Manager

Debian/UbuntuRHEL/CentOSFedora

sudo apt-get install git-lfs

sudo yum install git-lfs

sudo dnf install git-lfs

Download and Run Installer Download the latest Git LFS Windows installer and follow the setup instructions.

Initialize Git LFS Run the following command in your terminal to complete the setup:

git lfs install --skip-smudge

Project Setup¶

You first need to set up a project and initialize it:

mkdir MyNewCalyprProject
cd MyNewCalyprProject
git init
git drs init

Now that you have initialized your project you have created a very primitive Git Large File Support (LFS) backed git repository.

Download Gen3 API Credentials¶

To use the git-drs, you need to configure git-drs with API credentials downloaded from the Profile page.

Log into the website. Then, download the access key from the portal and save it in the standard location ~/.gen3/credentials.json

Gen3 API Key

Gen3 Credentials

Configure a git-drs repository with a Gen3 Credential.¶

Now that you have a Gen3 API credential, you can attach the credential to your git-drs repository by adding it as a drs remote.

git-drs requires a bucket name and a project id to defined in this command.

The bucket name is the name of the s3 bucket that you plan to upload your data to. This bucket must be configured inside the calypr instance. contact to setup a calypr bucket.

the project id must be in the form ORGANIZATION-PROJECTNAME.

From the command line from within your new porject, run the git-drs remote add command:

Example CommandMac/LinuxWindows

git-drs remote add gen3 <profile_name> \
    --cred=<path_to_credential.json> \
    --project <project_name>
    --bucket <bucket_name>

git-drs remote add gen3 cbds \
    --cred=~/Downloads/credentials.json \
    --project testProgram-testProject \
    --bucket testBucket

git-drs remote add gen3 cbds \
    --cred=C:\Users\demo\Downloads\credentials.json \
    --project testProgram-testProject \
    --bucket testBucket

You can confirm your configuration and access by listing your remotes:

git drs remote list

This will show your configured profiles and the projects you have access to.

Remaining Execution¶

From this point forward, git-drs functions exactly like git-lfs, see git-lfs documentation for more in depth documentation.

An example of uploading a file to calypr and downloading it can be viewed below:

Upload Files¶

# Track files
git lfs track "*.bam"
git add .gitattributes

# Add and commit files
git add my-file.bam
git commit -m "Add data file"
git push

Downloading existing files¶

git clone mylfsrepo
cd mylfsrepo
git drs init
git drs remote add gen3 myProfile --cred ~/.gen3/credentials.json --project cbds-my_lfs_repo --bucket cbds
git lfs pull -I "*.bam"