galaxyproject/SARS-CoV-2

This repository has been archived on 07/Feb/2023
Stars
128
Rank 281,044 (Top 6 %)
Language
Jupyter Notebook
License
MIT License
Created over 4 years ago
Updated almost 2 years ago

galaxyproject/SARS-CoV-2

galaxyproject

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures

home	heroText	description
true	Global platform for the analysis of SARS-CoV-2 data: Genomics, Cheminformatics, and Proteomics	Using open source tools and public cyberinfrastructure for transparent, reproducible analyses of viral datasets.

Visit our new SARS-CoV-2 surveillance site!

As of January 2022 this site will no longer be updated. Please visit our new site at https://galaxyproject.org/projects/covid19/ for the latest information on our surveillance efforts!

The goal of this resource is to provide publicly accessible infrastructure and workflows for SARS-CoV-2 data analyses. We currently feature three different types of analyses: Genomics, Cheminformatics, and Proteomics.

The analyses have been performed using the Galaxy platform and open source tools from BioConda. Tools were run using XSEDE resources maintained by the Texas Advanced Computing Center (TACC), Pittsburgh Supercomputing Center (PSC), and Indiana University in the U.S., de.NBI, VSC cloud resources and IFB cluster resources on the European side, STFC-IRIS at the Diamond Light Source, and ARDC cloud resources in Australia.

galaxy

Data intensive science for everyone.

training-material

A collection of Galaxy-related training material

tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

ansible-postgresql

An Ansible role for managing a PostgreSQL server

galaxy-hub

Galaxy Community Hub

planemo

Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.

bioblend

A Python library for interacting with the Galaxy API

ansible-slurm

Ansible role for installing and managing the Slurm Workload Manager

admin-training

Galaxy Admin Training

ansible-galaxy

An Ansible role for managing a Galaxy server

cloudlaunch

Easily launch cloud applications.

galaxy-helm

Minimal setup required to run Galaxy under Kubernetes

pulsar

Distributed job execution application built for Galaxy

cloudman

Easily create and manage compute clusters on any Cloud.

tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.

usegalaxy-playbook

Ansible Playbook for usegalaxy.org

iwc

Galaxy Workflows maintained by the Intergalactic Workflow Commission

ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.

gxadmin

Handy command line utility for Galaxy administrators 🚀

galaxy-language-server

Galaxy Language Server to help in Galaxy (https://galaxyproject.org/) tool wrappers development.

ansible-common-roles

A collection of simple Ansible roles for common (mostly system) tasks

galaxy-cloudman-playbook

Build components for CloudMan, Galaxy on the Cloud, or Galaxy Server

blend4j

blend4j is a JVM partial reimplementation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.

ansible-galaxy-tools

An Ansible role for automated installation of tools from a Tool Shed into Galaxy.

gravity

Galaxy process management and system administration tools

total-perspective-vortex

Total Perspective Vortex provides an installable set of dynamic rules for the Galaxy application that can route entities (Tools, Users, Roles) to appropriate job destinations based on a configurable yaml file.

cargo-port

cache packages permanently

galaxy-lib

Subset of Galaxy (http://galaxyproject.org/) core code designed to be used as a library.

galaxy-beta1

Galaxy Github repository BETA 1. May be destroyed and recreated if post-conversion problems are found (but post-conversion commits on this repo will be reapplied to any recreations). Scary disclaimer aside, so far so good! Full details:

awesome-galaxy

Awesome resources related to Galaxy project

infrastructure-playbook

Ansible playbook for managing Galaxy infrastructure. For the playbook managing Galaxy itself, see https://github.com/galaxyproject/usegalaxy-playbook/

usegalaxy-tools

usegalaxy.* common tools

ansible-postgresql-objects

A simple Ansible role for managing PostgreSQL objects (users, groups, databases, and privileges).

ansible-galaxy-extras

Ansible roles to configure assorted compontents for an Ubuntu VM or container configured with https://github.com/galaxyproject/ansible-galaxy with production services including nginx, uwsgi, supervisor, protftp, and slurm.

ansible-cvmfs

An Ansible role for installing and configuring CernVM-FS (CVMFS)

planemo-machine

A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.

idc

Simon's Data Club - Reference data for Galaxy servers

galaxy-docker-k8s

An Ansible playbook for building a Galaxy container for Kubernetes.

planemo-monitor

Planemo scripting to monitor repositories and register tool containers.

gxformat2

Galaxy Workflow Format 2

ansible-cloudman-image

An Ansible role for building a machine image for CloudMan.

starforge

Build Galaxy dependencies, wheels, and other things, in Docker (and other things)

Galaxy-XSD

Galaxy XML tool wrapper XSD

cloudlaunch-ui

A user interface for the cloudlaunch app

small-scale-galaxy-admins

ansible-nginx

An Ansible role for managing an nginx server.

tiaas2

Reusable Training Infrastructure as a Service

galaxy_codex

Galaxy Communities Dock aka Galaxy Codex: catalog of Galaxy resources (tools, training, workflows)

galaxy-flavor-testing

Travis scripts to unify and ease the testing of Galaxy favors

galaxy-upload

Galaxy Upload Utility for the CLI

planemo-ci-action

Test, deploy, or lint changed Galaxy tools or workflows using Planemo.

blend4php

A PHP API for interacting with Galaxy

galaxy-tours

Collection of Galaxy-tours

ansible-galaxy-toolshed

An Ansible role for managing a Galaxy (http://galaxyproject.org) Tool Shed server. For a role to install Galaxy itself, see https://github.com/galaxyproject/ansible-galaxy

sequence_utils

Galaxy's sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.

usage-metering

Scripts and queries for inspecting Galaxy usage data.

Jupyter Notebook

ansible-pulsar

An Ansible role for managing a Pulsar (https://github.com/galaxyproject/pulsar) server.

galaxy-tool-repository-template

seek-bzip2

ansible-proftpd

Ansible role for installing and configuring ProFTPD for Galaxy

wheelforge

Build Python wheels from recipes using cibuildwheel

edam_data

A Python-packaged version of EDAM Ontology Data (http://edamontology.org/)

ansible-interactive-environments

An Ansible role for installing Galaxy Interactive Environments

ptdk

Webserver for Planemo Training Development Kit

docker-galaxy-requirements

Galaxy requirements for installing Tools from the Tool Shed

galaxy-maps

dockstore-galaxy-interface

Dockstore Plugin for Galaxy Workflows

cloudauthz

gx-it-proxy

gx-tool-db

An application for managing structured metadata about Galaxy tools.

ansible-miniconda

An Ansible role for managing a Miniconda installation.

ansible-galaxy-os

An Ansible role is for configuring the base operating system useful for running Galaxy.

tpv-shared-database

A shared database of rules for Total Perspective Vortex used by the usegalaxy.* federation.

gxabm

Scripts for automating tasks in Galaxy

starforge-recipes

Build recipes for Galaxy Starforge

pulsar-helm

Helm charts for Pulsar

ansible-mailman3

Ansible role for installing and managing the GNU Mailman 3 suite

p4

Proper Prior Planning Prevents Poorly Performed PRs...Probably

conda-iuc

Conda recipes maintained by the Galaxy IUC.

ansible-opendkim

Ansible role for installing, configuring, and managing OpenDKIM

jxtx

homebrew-toolshed

Homebrew tap for Tool Shed packages. (Experimental and work in progress).

ansible-cloudman-database

An Ansible role for setting up PostgreSQL database for use with Galaxy CloudMan.

hack-the-galaxy-gcc2017

ansible-tiaas2

Ansible role for deploying TIaaS2

cloudlaunch-registry

An application registry for CloudLaunch

galaxyproject.github.io

Informational repository, highlighting the code offerings of Galaxyproject

ansible-cloudman-galaxy-setup

This role is used to setup Galaxy for use with CloudMan.

gxyarchiver

ansible-trackster

An Ansible role for setting up Galaxy Trackster.

galaxy_mentor_network

Galaxy Mentor Network

homebrew-tap

A Homebrew (http://brew.sh/) tap for Galaxy (http://galaxyproject.org/) related software.

gxy.io

The gxy.io link shortening service

TIS_methods_review

Jupyter Notebook

galaxy-test-data

Test data files used by Galaxy.

gsoc

galaxy-merger

Script that automates merging Galaxy.

galaxytutorial-ismb17

gx-tool-db-project

A project containing database created with the gx-tool-db tool.

alignment-pipeline