Galaxy_Training_Barcelona_2020

Usefull scripts and exercises from Galaxy Admin Training Barcelona 2020, slides here: https://github.com/galaxyproject/dagobah-training/tree/2020-barcelona

Software support

Galaxy versions are only supported for 1y. Update is mandatory!

Ansible

Ansible tutorial: https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible/tutorial.html#your-first-playbook-and-first-role

Ansible Glaxy repo: https://galaxy.ansible.com/

Ansible basic inventory structure:

.
├── group_vars
│   └── my_hosts.yml
├── hosts
├── playbook.yml
└── roles
    └── my-role
        ├── defaults
        │   └── main.yml
        ├── files
        │   └── test.txt
        ├── tasks
        │   └── main.yml
        └── templates
            └── test.ini.j2

Execute ansible playbook from inventory: ansible-playbook -i hosts playbook.yml

Execute ansible playbook from inventory and enumerate differences: ansible-playbook -i hosts playbook.yml --check --diff

List host metadata: ansible -i hosts -m setup my_hosts | less

Add some roles from Ansible Galaxy: ansible-galaxy install -p roles/ geerlingguy.git

Install Galaxy

Install Galaxy tutorial: https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html

Tool management

Toolshed tools now:

• Can be installed with conda
• Are Singualrity and Docker compatible
• There are automatic importers for perl, python y R tools: ephemeris
• Replicate other Galaxy instances by exporting and installing their tools and workflows list with ephemeris

Biocontainers

Biocontainers surveilance and build containers in real time of many bioinformatics repositories Galaxy is compatible with both Singularity and Docker containers Tools from the toolshed create their own conda environment for each one individually

User management

Users: https://training.galaxyproject.org/training-material/topics/admin/tutorials/users-groups-quotas/slides.html#6

Auth Methods

i.e., LDAP

slides: https://training.galaxyproject.org/training-material/topics/admin/tutorials/external-auth/slides.html#1

example of configuration: https://training.galaxyproject.org/training-material/topics/admin/tutorials/external-auth/tutorial.html

Reference Data and CVMFS

Slides: https://training.galaxyproject.org/training-material/topics/admin/tutorials/cvmfs/slides.html#1

example of configuration: https://training.galaxyproject.org/training-material/topics/admin/tutorials/cvmfs/tutorial.html

My previous repo with ansible installing Galaxy with CVMFS: https://github.com/MiguelJulia/GCC2019_GalaxyAnsibleDeplyoment_CVMFS

Job configuration

Slides: https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/slides.html#1

example config file: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/job_conf.xml.sample_advanced

example with SLURM: https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html

Pulsar (for running jobs on remote resources)

Slides: https://galaxyproject.github.io//training-material/topics/admin/tutorials/pulsar/slides.html#1

Example: https://galaxyproject.github.io//training-material/topics/admin/tutorials/pulsar/tutorial.html

Bioblend (Galaxy API)

Slides: https://training.galaxyproject.org/training-material/topics/dev/tutorials/bioblend-api/slides.html#1

Examples: https://mybinder.org/v2/gh/nsoranzo/bioblend-tutorial/master?filepath=bioblend_histories.ipynb

Reporting

Basic conf: https://training.galaxyproject.org/training-material/topics/admin/tutorials/reports/tutorial.html

gxadmin: https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/slides.html#1

exercise: https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html

Monitoring

Slides: https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/slides.html#1

Example: https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html

Data management

Slides: https://training.galaxyproject.org/training-material/topics/admin/tutorials/object-store/slides.html#1

Exercise: https://training.galaxyproject.org/training-material/topics/admin/tutorials/object-store/tutorial.html