GGA

View the Project on GitHub galaxy-genome-annotation/galaxy-genome-annotation.github.io

Galaxy Genome Annotation

GGA is a group of projects focused on supporting genome annotation inside Galaxy.

Production Ready

docker-galaxy-genome-annotation

GitHub Contributors License

Galaxy Docker repository with tools for Genome Annotation. The image is built with tools for Assembly (Spades, Mira), Structural Prediction (Glimmer, Augustus), Functional Prediction (BLAST+, InterProScan, BLAST, Diamond, Blast2GO), various Utilities (FASTA manipulation tools, EMBOSS), tools for Comparative Genomics (CD-Hit, ClustalW, AntiSmash, mummer), and finally Annotation & Visualization tools (Apollo Tools, JBrowse-in-Galaxy, JBrowse-in-Galaxy Extras, Tripal Admin tools, Circos)

docker-tripal

GitHub Contributors License

A production ready Docker image for Tripal v2.x and v3.x.

docker-jbrowse

GitHub Contributors License

A production ready Docker image for JBrowse.

docker-chado

GitHub Contributors License

A production ready Docker image for Chado database. The image is built automatically using SQL dumps produced by chado-schema-builder, including up-to-date ontologies.

dockerized-gmod-deployment

GitHub Contributors License

If customizing the docker-galaxy-genome-annotation image isn’t your style, this is a preconfigured deployment of Galaxy + Apollo + Chado + Tripal + JBrowse + JBrowse REST API + PostGraphQL + JBrowse GraphQL Experiment all as a docker-compose.yml

python-apollo

GitHub Contributors License

Python library for talking to Apollo API. This includes the experimental Arrow Apollo client.

python-tripal

GitHub Contributors License

A Python library for interacting with Tripal

python-chado

GitHub Contributors License

A Python library for interacting with Chado database

galaxy-tools

GitHub Contributors License

Galaxy tools for Genome Annotation.

galaxy-circos-tool

GitHub Contributors License

Convenient wrapper around Circos allowing building of a huge variety of highly configurable Circos plots. This will eventually be merged into the IUC repository.

Experiments

apollo-git-backup

GitHub Contributors License

Backup an apollo instance to a git repository

apollo-google-docs-integration

GitHub Contributors License

Experimental work for a plugin to allow referencing data from Apollo. For genomes which are re-opened / re-numbered / etc. between drafting and publication, it can be extremely helpful to reference persistent identifiers.

Support

This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)