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iPlant Collaborative Open Source

Login: iPlantCollaborativeOpenSource

Company: null

Location: Our Virtual Organization includes people from The University of Arizona, Cold Spring Harbor Laboratory, The University of Texas at Austin, and more.

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Blog: http://www.cyverse.org/open-source

Members

Repositories

Advanced_iPlant: Materials and scripts for the API-focused "Advanced iPlant" workshop series
agave-cli-docker: iPlant-flavored release of Agave API command line interface
ansible: Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy. Avoid writing scripts or custom code to deploy and update your applications? automate in a language that approaches plain English, using SSH, with no agents to install on remote systems.
atmo-ansible-callback: An reference callback for use within subspace
atmo-cl: A command line interface for Atmosphere.
Atmodroid: iPlant Atmosphere for Android
atmosphere-apiary-docs: API Documentation for Atmosphere
atmosphere-logstash: Logstash configuration files used by Atmosphere.
atmosphere-theme: null
Badge-Admin: A collection of scripts for badgekit database management
beanstalk: Clojure Beanstalk Client
beanstalk-client: C/C++ beanstalk client
biodiversity: null
BTI_iPlant_RNAseq: Updates required to support integration into the iPlant DE
cas: Jasig CAS - Single Sign On for the Web
CAS-Extensions: Custom extensions to CAS
chinstrap: null
clj-cas-login: A Clojure library used to obtain service tickets from a CAS server.
coge-rest: REST API to CoGe
cogex: CoGe Database Client Library
confluence-client: A Confluence interface for the Discovery Environment
crushbone: Atmosphere install, test, configuration, analysis and utility scripts.
datamatch: Datamatch, aka Lopper, is tool to prune phylogenetic datasets to a common list of taxa.
datastore-public: A web-based file browser for iRODS with metadata-based templating.
data-webapp: iPlant Data Web application
de-buggalo: Special purpose phylogenetic tree processing service.
Demonstrate: Demonstrate takes outputs from the Validate known-truth pipeline for iPlant Collaborative and produces a single data set and graphics.
DiscoveryEnvironmentShared: Libraries shared by the DiscoveryEnvironment and DiscoveryEnvironmentBackend repositories.
django-deadwood: A service to keep track of dependencies
django-iplant-boilerplate: This repository can be used as boilerplate django, as well, it can be installed and used as a reusable app for Authentication and more.
django-rest-swagger: Swagger Documentation Generator for Django REST Framework
django-sslserver: A SSL-enabled development server for Django
dnalc_fAPI: Foundation API Apps and utilities used by the iPlant DNA Subway
dnalc_fAPI_apps: DNALC's iPlant foundation API apps
dnasub_docker_base: Lonestar4 compatibility base for DNA Subway Agave apps
dnasubway-apps: Docker and Singularity-compatible versions of DNA Subway apps
docker-builds: A place to put docker build files
Drupal-Rods: Store and retrieve files on iRODS from Drupal
dtwo: A client for stratosphere.
epel: null
euca2ools: Eucalyptus client API tools. Compatible with Amazon EC2 and IAM APIs
FileQuirks: FileQuirks is a system which enables you to check the type of your raw text file containing biological data.
filequirks-db-vagrant: null
graphios: A program to send nagios perf data to graphite (carbon) / statsd / librato / influxdb
gwt-taglist: null
host_watch: null
hyper-stats: A service to collect VM stats from libvirt.
hyper-stats-ansible: Ansible playbook to deploy hyper-stats metrics aggregation
IBP: Integrated Breeding Platform
idpauthn: Identity Provider Authentication module.
interproscan-agave: Repo for scalable InterproScan via Agave and the TACC Parametric Launcher
iPlant-Atmosphere: null
iPlantFoundationAPIAdapter: null
iplant-ncl: iPlant repackaging of NEXUS Class Library
iPlant_phyloviewer: GWT-based phylogenetic viewer
iplant-treerec: Back end services that power iPlant's Tree Reconciliation.
iRODS3.2-custom: This is a custom version of iRODS version 3.2 with some SQL optimization related to tickets.
irods-3.3.1-iplant: This is a fork of the iRODS based on the 3.3.1 released.
iRODS3.3-iplant: This is a version if iRODS 3.3 with custom patches applied.
irods4-upgrade-env: A collection of docker containers that mimic our production environment intended to test our iRODS 4 upgrade process
irods_connection_counter: A user connection counter for irods
irodsfile: iRODS File handling utilities.
irods-setavu-plugin: An iRODS plugin that provides a microservice for setting AVUs
irods-vagrant: Sets up a Vagrant VM running Ubuntu 14.04 LTS with a minimal iRODS install.
jargon: Jargon core libraries
jlrproxytoolkit: Java Language Reflection Proxy Toolkit for use with Mule.
jwt.py: null
Korma: Tasty SQL for Clojure.
libcloud: Apache Libcloud is a Python library which hides differences between different cloud provider APIs and allows you to manage different cloud resources through a unified and easy to use API
McKay_DE_utils: Collection of Perl wrappers and related utilities for DE Apps integrated by Sheldon McKay
muletoolkit: A toolkit for classes used within Mule.
Nagios-Plugin-ServiceStatus: A Nagios plugin that uses /sbin/service to determine the status of an initd service.
ncbi-sra-submit: This project contains python scripts and XML templates for generating SRA submissions from iPlant Collaborative Data Store metadata and a Bio Project input directory.
notifications-db-vagrant: null
nrpe: NRPE Agent
optimal-optimization: null
pac4j-oauth-iplant: null
perpetually-updated-trees: null
phyloparser: A library to parse common phylogenetic formats.
phyloviewer: GWT phylogenetic tree viewer
pok: Configuration should be easy.
psycopg2_userdefined: Get the oid in postgresql for a user defined type using psycopg2.
python-irodsclient: A python API for iRODS
python-keystoneclient: null
python-snowflakeclient: Another python snowflake client.
rabbitmq: null
rfive: Drop-in Fabric deploy for libcloud
Robotframework-MongoDB-Library: A library for interacting with MongoDB from RobotFramework
saml: Library for create assertions in Security Assertion Markup Language (SAML) format.
Satellite: Uptime monitoring service for iPlant products, similar to Pingdom.
securitymodule: A Mule module for securing service-endpoints with SAML assertions.
securitytoolkit: Security and Authentication related toolkit for working with Shibboleth & SAML.
Sheldon_DE_utils: perl scripts and libraries supporting Sheldon McKay DE Applications
skywalker: Thrift definitions for Atmosphere.
skywalker-python: Generated Python skywalker thrift.
skywalker-python.tornado: Generated Python tornado skywalker thrift.
skywalker-python.twisted: Generated Python twisted skywalker thrift.
skywalker.thrift: Thrift IDL for Stratosphere.
snowflake: Snowflake is a network service for generating unique ID numbers at high scale with some simple guarantees.
status-site: null
stratosphere: A service for rtwo.
swish: Ansible deployment for Badgekit Admin UI & API
tardis-analytics: Tracking and Retreiving Data Interface Service, iPlant's provenance analytics api
tardis-apis: Tracking and Retreiving Data Interface Service, iPlant's provenance collector api
TNRS: The Taxonomic Name Resolution Service is a free utility for correcting and standardizing plant names.
Tree-Reconciliation-Ontology: null
tr-standalone: iPlant Tree Reconciliation Viewer
Validate: Known-truth testing for genome-wide association tools; updated for python from the ktar project

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.