Oregon Health and Science University Computational Biology

funnel

Funnel is a toolkit for distributed task execution via a simple, standard API.

dos_connect

Data Object Registry Connect

compbio-galaxy-wrappers

OHSU Galaxy wrappers.

py-tes

Python SDK for the GA4GH Task Execution API

regulon-enrichment

bridge2ai-jupyter

Docker Image for JupyterHub with restricted download and tensorflow/pytorch

bergamot

data-import-test

Collection of scripts and documentation for importing S3 data into the Gen3 system

hapi-fhir-auth

HAPI FHIR authorization hook for the ACED data commons

homebrew-formula

homebrew tap for OHSU Comp Bio tools

openstack_k8s

Utilities to provision kubernetes clusters in an on premises openstack environment.

sower

Job dispatcher for Kubernetes

bam_readgroup_to_json

Extract a readgroup from a BAM, and write it as json

biobambam-docker

containers

decoupleR

R package to infer biological activities from omics data using a collection of methods.

decoupler_workflow

Snakemake decoupleR wrapper

decoupleRBench

Package to benchmark methods from decoupleR

docker-centos7-slurm

Slurm Docker Container on CentOS 7

drs_downloader

Download tool for AnVIL/TDR data identified by DRS URIs and Google

fence-multipart

AuthN/AuthZ OIDC Service

glasswing-status

Uptime/downtime monitor and status page for CBDS

hatchery

hop-covid-models

nextflow

A DSL for data-driven computational pipelines

nf-canary

A minimal Nextflow workflow for testing infrastructure.

openapi-test-runner

An application allowing the TES servers to test their conformance to TES Specifications

pyinstaller

Freeze (package) Python programs into stand-alone executables

synthesis

vrs_anvil_toolkit

Extract clinical variant interpretations from VCF using GA4GH VRS IDs