Galaxy
List pointers to useful information about Galaxy under the appropriate heading here.
Galaxy UI Development Gitlab wiki page
Container images
- Our internal SAE Galaxy images are found at: https://code.ornl.gov/rse/galaxy
- [DEPRECATED][B. Gruening's DockerHub with Galaxy images](https://hub.docker.com/r/bgruening/galaxy-stable/)
- This image is out-dated and showing many security vulnerabilities
Remote data
- https://gcc2021.sched.com/event/ih0X/using-galaxy-file-source-plugins-to-work-with-remote-data-including-applications
- https://gcc2021.sched.com/event/jm8N/galaxy-cloudstor-integration-linking-national-resources-for-secure-data-transfer-between-services
- https://github.com/galaxyproject/galaxy/issues/11853
Remote compute
- https://gcc2021.sched.com/event/jm5q/hpc-back-end-runner-for-massive-sars-cov-2-samples-processing
- https://gcc2021.sched.com/event/kGd5/th-55-augmenting-galaxy-with-gpu-support-for-speeding-up-scientific-applications
- https://gcc2021.sched.com/event/kGdB/th-58-cloudforest-dockerized-galaxy-as-a-platform-for-an-integrated-phylogenomics-software-workflowhttps://docs.google.com/presentation/d/1TaWmxet80B0REDGYFL3z4GBDmANtr1j_uFvZMIkrBF0/edit#slide=id.g3bc2ffc0d6_0_51
- Example of docker-compose for Galaxy + Pulsar:
Machine learning
- https://gcc2021.sched.com/event/jm7S/galaxy-ml-an-accessible-reproducible-and-scalable-machine-learning-toolkit-for-biomedicine
- https://gcc2021.sched.com/event/k5MW/w-48-gpu-enabled-jupyterlab-notebook-for-deep-learning-using-tensorflow-in-galaxy
Science Workflows
- https://gcc2021.sched.com/event/ihp0/analysis-of-microscopy-data-in-galaxy
- https://gcc2021.sched.com/event/jm8r/ximg-chess-a-galaxy-based-science-gateway-for-x-ray-diffraction-imaging-and-microstructure-modeling
Interactive tools (e.g. Jupyter)
- https://gcc2021.sched.com/event/k5MT/w-311-galaxylab-a-jupyterlab-extension-for-interactive-graphical-and-programmatic-access-to-galaxy
- https://gcc2021.sched.com/event/jm93/interactive-tools-in-galaxy-on-kubernetes
Tool development
Galaxy internals
- https://gcc2021.sched.com/event/jm85/modernizing-the-galaxy-backend-data-model
- https://gcc2021.sched.com/event/jm88/modernizing-the-galaxy-backend-typing-and-the-api
- https://gcc2021.sched.com/event/jm8B/modernizing-the-galaxy-backend-typing-and-dependency-injection
- https://gcc2021.sched.com/event/jm8E/modernizing-the-galaxy-backend-a-task-framework
Galaxy development roadmap and future
Some of these documents are older but I don't think they are "outdated". They are the most recent documentation I can find.
- Pulsar https://github.com/galaxyproject/galaxy/issues/11824
- Galaxy Workflows https://docs.google.com/presentation/d/1R7gkC603gne59IlP31dACn72XAGRfC63ZdHaA9q5Oh0/edit#slide=id.gf7f57ad2ac_0_0
- Galaxy backend goals https://github.com/galaxyproject/galaxy/issues/11824
- Galaxy: The next two years https://hackmd.io/J8km_DwbTg2QzUkv4ijCmw
- Galaxy project direction. They have recently switched to using working groups: https://galaxyproject.org/community/wg/