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README.md

wreleaser (WARP releaser) is a simple CLI tool for querying WARP releases.

🧬 Overview

WARP maintains and releases over two dozen cloud-optimized pipelines for biological data processing. Finding information for various pipeline releases via the repo's web interface is clunky and tedious.

wreleaser serves as a wrapper around the GitHub Releases API specifically for WARP releases.

How does it work?

On initial invocation wreleaser will hit the GitHub Releases API for WARP and cache all of the releases in $HOME/.wreleaser/cache.json.

WARP doesn't release frequently so to avoid having to hit the API regularly wreleaser will return results from the cache by default.

To reset your cache you can run wreleaser reset.

⚙️ Installation

Option 1

Make sure you have Go installed (download). Then install wreleaser with the go get command:

go install github.com/broadinstitute/warp/wreleaser@latest

Option 2

We have binaries available here for linux/amd64 and darwin/amd64.

If you have a different OS/Architecture please clone this repo and run go build from this directory to compile the binary for your system.

Once the binary is on your machine please add it to a location in your $PATH.

⭐ Quickstart

$ wreleaser --help

$ wreleaser is a lightweight CLI to list, query and download various WARP releases

Currently available pipelines:
        - AnnotationFiltration
        - Arrays
        - BroadInternalRNAWithUMIs
        - BroadInternalArrays
        - BroadInternalImputation
        - BroadInternalUltimaGenomics
        - CEMBA
        - CheckFingerprint
        - CramToUnmappedBams
        - ExomeGermlineSingleSample
        - ExomeReprocessing
        - ExternalExomeReprocessing
        - ExternalWholeGenomeReprocessing
        - GDCWholeGenomeSomaticSingleSample
        - IlluminaGenotypingArray
        - Imputation
        - JointGenotyping
        - JointGenotypingByChromosomePartOne
        - JointGenotypingByChromosomePartTwo
        - MultiSampleArrays
        - MultiSampleSmartSeq2
        - MultiSampleSmartSeq2SingleNucleus
        - Optimus
        - ReblockGVCF
        - RNAWithUMIsPipeline
        - SmartSeq2SingleNucleus
        - SmartSeq2SingleSample
        - UltimaGenomicsWholeGenomeGermline
        - UltimaGenomicsJointGenotyping
        - ValidateChip
        - VariantCalling
        - WholeGenomeGermlineSingleSample
        - WholeGenomeReprocessing

Usage:
  wreleaser [command]

👀 Examples

Commands

wreleaser info all

Displays release information for all pipelines

Flags:

  • -l, --latest Retrieve only the latest releases for each pipeline
  • -h, --help Display help text
  • --output Pipe stdout to file
$ wreleaser info all # Gets all the releases for every pipeline

$ wreleaser info all --latest # Gets only the latest releases for every pipeline

$ wreleaser info all --latest --output=foo.json # Gets the latest releases for every pipeline and write it to foo.json

wreleaser info list

Display release information for one or more pipelines

Flags:

  • -l, --latest Retrieve only the latest releases for each pipeline
  • -v, --version Specific version number of pipeline to retrieve (can only use for single pipeline arguments)
  • -h, --help Display help text
  • --output Pipe stdout to file
$ wreleaser info list Arrays # Gets all the releases for the Arrays pipeline

$ wreleaser info list Arrays --version=v2.3.1 # Gets the release for Arrays pipeline version v2.3.1

$ wreleaser info list Arrays ExomeGermlineSingleSample # Gets all releases for Arrays and ExomeGermlineSingleSample pipelines

$ wreleaser info list CEMBA Optimus --latest # Gets the latest releases for CEMBA and Optimus pipelines

$ wreleaser info list CEMBA Optimus --latest --output=foo.json # Gets the latest releases for CEMBA and Optimus pipelines and write it to foo.json

wreleaser reset

Clear the directory that caches WARP releases

Default directory is $HOME/.wreleaser/cache.json but you can choose to write/clear cache with the --cachedir flag for any command

Flags:

  • h, --help Display help text
  • --cachedir Directory to cache release information
$ wreleaser reset # Clears the cache at $HOME/.wreleaser/cache.json

$ wreleaser reset --cachedir=/path/to/custom # Clears the cache at /path/to/custom

💥 Troubleshooting

If you have any questions about this tool or need some help configuring it please reach out at [email protected].