bit.ly/galaxyadmin
bit.ly/adminvms
bit.ly/gadminchat
Galaxy Release Schedule
3 releases per year: January, May and September
Install Galaxy using Ansible
sudo pip install ansible
git clone https://github.com/ARTbio/GalaxyKickStart
cd GalaxyKickStart
git checkout 2018-gccbosc
ansible-galaxy install -r requirements_roles.yml -p roles –force
$ sudo su galaxy
$ vi /srv/galaxy/config/galaxy.yml
# Add the following line under galaxy: section
admin_users: your@email.address
$ exit # change back to ubuntu user
$ sudo supervisorctl restart galaxy:
galaxy.ansible.com/explore#
Time | Topic | Links | Instructor |
---|---|---|---|
09:00 | Welcome and introduction | Slides | (Č) |
09:15 | Deployment and platform options | Slides | (Č) |
9:30 | Using Ansible to deploy Galaxy | Slides, Exercise | (E)(G) |
10:20 | Extending installation | Slides, Exercise | (G) |
10:40 | Defining and importing genomes, Data Managers | Slides, Exercise | (E) |
11:00 | Galactic Database | Slides | (M)(N) |
11:15 | Web Servers nginx/Apache | Slides | (M)(N) |
11:30 | Close Morning Session |
https://github.com/galaxyproject/dagobah-training/blob/2018-gccbosc/sessions/05-reference-genomes/ex1-reference-genomes.md#exercise-3-install-a-datamanager-from-the-toolshed
https://github.com/galaxyproject/dagobah-training/blob/2018-gccbosc/sessions/14-ansible/ex2-galaxy-ansible.md
Galaxy admin -> local data: Create DBKey and Reference Genome – fetching
Install dbkey from saccer2 data_manager_fetch_genome_dbkeys_all_fasta
Install BWA data_manager_bwa_mem_index_builder
https://ephemeris.readthedocs.io/en/latest/
Admin -> create bwa index
Second Session
ubuntu@2018-gcc-training-0:~⟫ sudo vim /srv/galaxy/config/galaxy.yml
In /srv/galaxy/config/galaxy.yml
, uncomment #nginx_x_accel_redirect_base: False
and change it to nginx_x_accel_redirect_base: /_x_accel_redirect
. Remember, this file is owned by the galaxy user so be sure to use sudo -u galaxy
when editing it.
https://github.com/galaxyproject/dagobah-training/blob/2018-gccbosc/sessions/03-production-basics/ex3-nginx.md
sudo supervisorctl restart nginx galaxy:
Google’s PageSpeed Tools can identify any compression or caching improvements you can make.
If configuring SSL (out of scope for this training), out-of-the-box SSL settings are often insecure!
Use the Mozilla SSL config generator to create a default config and Qualys SSL Server Test to check it.
https://planemo.readthedocs.io/en/latest/
https://planemo.readthedocs.io/en/latest/readme.html
https://planemo.readthedocs.io/en/latest/writing_cwl_appliance.html?highlight=write%20appliance
$ planemo test –no-container –engine toil seqtk_seq.cwl
galaxy-tool-test
planemo o
#this will open the browser
https://planemo.readthedocs.io/en/latest/writing_advanced.html
https://stats.galaxyproject.org/login
https://grafana.com
https://telescope.galaxyproject.org
cd /srv/galaxy/server/lib/galaxy/jobs/runners
Plugins
Correspond to job runner plugins in lib/galaxy/jobs/runners
Plugins for:
- local
- Slurm (DRMAA subclass)
- DRMAA: SGE, PBS Pro, LSF, Torque
- HTCondor
- Torque: Using the
pbs_python
library - Pulsar: Galaxy’s own remote job management system
- Command Line Interface (CLI) via SSH
- Kubernetes
- Go-Docker
- Chronos
https://galaxyproject.github.io/dagobah-training/2018-gccbosc/15-job-conf/job_conf.html#3
https://research.cs.wisc.edu/htcondor/
Need a shared file system, nfs, ceph and etc.
Exception is Pulsar!
sudo cat job_conf.xml.sample_basic <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <destinations> <destination id="local" runner="local"/> </destinations> </job_conf>
https://docs.galaxyproject.org/en/master/admin/jobs.html#dynamic-destination-mapping
https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
http://galaxyproject.github.io/training-material/topics/admin/tutorials/connect-to-compute-cluster/slides.html#1
https://github.com/galaxyproject/galaxy-hub/blob/master/src/galaxy-updates/2018-03/index.md
https://pulsar.incubator.apache.org/
http://galaxyproject.github.io/training-material/topics/admin/tutorials/connect-to-compute-cluster/slides.html#13
https://github.com/galaxyproject/galaxy-kubernetes
http://galaxyproject.github.io/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html#section-4—statically-map-a-tool-to-a-job-destination
Edit:/srv/galaxy/config/tool_destinations.yml
---
tools:
multi:
rules:
- rule_type: file_size
lower_bound: 16
upper_bound: Infinity
destination: slurm-2c
default_destination: slurm_cluster
default_destination: local_no_container
verbose: True
gdb
attach 28376
https://www.gnu.org/software/gdb/