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Duke Center for Genomic and Computational Biology

Login: Duke-GCB

Company: null

Location: Durham, NC

email: gcb-it@duke.edu

Blog: http://www.genome.duke.edu

Members

Repositories

2018-07-26-Duke: Data Carpentry for Genomics Workshop at Duke University, July 26-27, 2018
ansible-hackday: References and materials for GCB Informatics Ansible Hackday 2015-05-07
ansible-openstack: Deploy OpenStack on Bare Metal using Ansible
atmosphere: Where cloud lives.
atmosphere-ansible: Ansible instance deployment code for Atmosphere
bespin: Reproducible genomic workflows in the cloud
bespin-api: Web application for running workflows in the cloud
bespin-cli: Command line client for Bespin
bespin-cwl: CWL workflows for Bespin
bespin-jobtoken-generator: null
bespin-job-watcher: Allows users to receive job status notification updates for bespin-api
bespin-mailer: Bespin mail delivery service
bespin-ui: An ember.js application frontend for bespin-api
bespin-webapp-docker: Dockerfile and docker-compose script for running bespin-api and bespin-ui together
blinky: Tools and scripts for Grouper management
clank: null
cwl-freezer: Tool to snapshot and export a CWL document, and freeze its referenced Docker images
D4S2: Web service to facilitate notification and transfer of projects in DukeDS
DataC-HPC-genomics: Lesson on Cloud/HPC for genomics lessons
datadelivery-cli: Command line program to deliver s3 buckets to other users via D4S2
datadelivery-ui: An ember.js application frontend for d4s2
django-iplant-auth: All iPlant Auth schemes for use in a Django App
django-shibboleth-adapter: Adapter for integrating Shibboleth with the Django authentication system
docker-hackday: References and materials for GCB Informatics Docker Hackday 2016-03-10
docker-pipeline: Python tool to run docker containers in sequence, for reproducible computational analysis pipelines
DockerPostgresBackup: Backup a Postgres database running inside a docker container to a volume.
docker-wrapper: Wrapper scripts for docker volume access
drf-ember-backend: Backend code to enable Ember Data when using the Django REST Framework
drf-ember-frontend: Ember Addon to connect to Django REST Framework
drupal-security-check: null
DukeDSClient: Command line tool to upload a folder into a project on the duke-data-service
ElucidatorRestart: Elucidator Restart Service
GCB-Academy-2015-02-05: Materials for GCB Academy course Intro to Scientific Computing for Genomics, February 2015
gcb-ansible-roles: Ansible roles used by GCB Ansible Playbooks
GCB-Dockerfiles: Docker images for bioinformatic workflows that are built on Docker Hub under the DukeGCB organization.
gcb-web-auth: Django app that integrates Duke OAuth
GGR-cwl: CWL tools and workflows for GGR
helmod: Harvard Extensions for Lmod deployment
hook-build: Listens for github webhook, validates secret and runs a script
igsp_web_cookie: Daemon and Command-line tools for the IgspNet Authentication system.
iMADS: Web portal and supporting services that allow searching/creating TF predictions and preferences.
iMADS-worker: Worker for generating on-demand predictions using Docker and CWL in iMADS
informatics-support-youlab: Informatics support plan for You Lab
jupyter-scipy-tmpnb-server: null
lando: Lando's not a man, he's a system
lando-messaging: Messaging component of lando project
mariadb-docker-backup: Docker hackday output for backing up MariaDB via docker volumes
MMAP: Project_Lemur
MMAP-cwl: Common Workflow Language tool and workflow definitions for MMAP pipeline
MMAP-Docker: Docker images for containerizing MMAP
old-directory-pruner: null
openstack-ansible-host-prep: Ansible to set up hosts for OpenStack Ansible Deployment (OSA/OSAD)
Predict-TF-Binding: Python scripts for modeling and predicting TF-DNA binding using libsvm
Predict-TF-Preference: R scripts to predict preferences between two TFs using data from predict-tf-binding
prospatheia: Web-based effort reporting tool for GCB informatics
pypi-to-module: Creates an environment module from a package on pypi
python-web-base: null
rt-slack: Scrip for posting messages to Slack via webhooks
SciComp-Feb-2015: Website for the Feb 2015 GCB Academy course Introduction to Scientific Computing for Genomics
scicomp-hpc: null
SciComp-Mar-2016: Website for the March 2016 GCB Academy course Introduction to Scientific Computing for Genomics
SciComp-Materials: Materials for GCB Academy course Intro to Scientific Computing for Genomics
SciComp-Nov-2017: Website for the Nov 2017 GCB Academy course "Introduction to Scientific Computing for Genomics"
SciComp-Oct-2015: Website for the Oct 2015 GCB Academy course Introduction to Scientific Computing for Genomics
SciComp-Oct-2016: Website for the Oct 2016 GCB Academy course "Introduction to Scientific Computing for Genomics"
scicomp-python: Python lesson for GCB Academy: Intro to Scientific Computing
ScriptWrapper: Script that runs a command based on $PATH for hard coded scripts.
shell-genomics: null
SlurmFixer: Find and fix bad jobs in a slurm cluster
slurm-reporting: Small scripts and tools to report on usage of a cluster running SLURM
SLURM_Status: Script reporting status of a SLURM cluster.
SparkSlurm: Notes and scripts for running Spark on a slurm cluster.
Sun-Grid-Engine-Ansible: GridEngine deployment for SMRT Link cluster
svr-track-hub: Make+Docker to build a UCSCGB Track Hub
toil: Toil is a scalable, efficient, cross-platform pipeline management system, written entirely in Python, and designed around the principles of functional programming.
TrackHubGenerator: Python and Make tools for generating UCSC Track Hubs
troposphere: Atmosphere web client
WebDiskUsage: Small Flask application for parsing df output and displaying it in a web page

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.