Pinned Repositories
compbio-galaxy-wrappers
OHSU Galaxy wrappers.
cwl-tes
cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.
dockerized-tools
dos_connect
Data Object Registry Connect
funnel
Funnel is a toolkit for distributed task execution via a simple, standard API.
g2p-aggregator
Associations of genomic features, drugs and diseases
gdc-scan
A library for navigating and downloading from the GDC API
py-tes
Python SDK for the GA4GH Task Execution API
tesseract
Python lib for remote code execution via the GA4GH TES API
wdl-pcawg-bwa-mem-workflow
WDL implementation of https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow
Oregon Health and Science University Computational Biology's Repositories
ohsu-comp-bio/funnel
Funnel is a toolkit for distributed task execution via a simple, standard API.
ohsu-comp-bio/dos_connect
Data Object Registry Connect
ohsu-comp-bio/compbio-galaxy-wrappers
OHSU Galaxy wrappers.
ohsu-comp-bio/py-tes
Python SDK for the GA4GH Task Execution API
ohsu-comp-bio/regulon-enrichment
ohsu-comp-bio/bridge2ai-jupyter
Docker Image for JupyterHub with restricted download and tensorflow/pytorch
ohsu-comp-bio/vrs_anvil_toolkit
Extract clinical variant interpretations from VCF using GA4GH VRS IDs
ohsu-comp-bio/awesome-tes
A curated list of awesome GA4GH TES projects and programs
ohsu-comp-bio/data-import-test
Collection of scripts and documentation for importing S3 data into the Gen3 system
ohsu-comp-bio/homebrew-formula
homebrew tap for OHSU Comp Bio tools
ohsu-comp-bio/load-testing
Browser load testing using k6s
ohsu-comp-bio/sower
Job dispatcher for Kubernetes
ohsu-comp-bio/vrs-annotator
Annotates VCF Variants with VRS IDs
ohsu-comp-bio/containers
ohsu-comp-bio/decoupleR
R package to infer biological activities from omics data using a collection of methods.
ohsu-comp-bio/decoupler_workflow
Snakemake decoupleR wrapper
ohsu-comp-bio/decoupleRBench
Package to benchmark methods from decoupleR
ohsu-comp-bio/docker-centos-slurm
Slurm Docker Container on CentOS 7
ohsu-comp-bio/drs_downloader
Download tool for AnVIL/TDR data identified by DRS URIs and Google
ohsu-comp-bio/fence-multipart
AuthN/AuthZ OIDC Service
ohsu-comp-bio/gatk4_xml_prepare
Tools to auto-create XML files from GATK4 json descriptions.
ohsu-comp-bio/glasswing-status
Uptime/downtime monitor and status page for CBDS
ohsu-comp-bio/hatchery
ohsu-comp-bio/hop-covid-models
ohsu-comp-bio/idp-backups
Steps for backing up, migrating, and restoring IDP data
ohsu-comp-bio/nextflow
A DSL for data-driven computational pipelines
ohsu-comp-bio/nf-canary
A minimal Nextflow workflow for testing infrastructure.
ohsu-comp-bio/openapi-test-runner
An application allowing the TES servers to test their conformance to TES Specifications
ohsu-comp-bio/project-template
Example Repo Template for OHSU Comp Bio projects
ohsu-comp-bio/pyinstaller
Freeze (package) Python programs into stand-alone executables