Galaxy Conference – Admin 25/06/2018

bit.ly/galaxyadmin
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bit.ly/gadminchat

Galaxy Release Schedule

3 releases per year: January, May and September

Install Galaxy using Ansible

https://github.com/galaxyproject/dagobah-training/blob/2018-gccbosc/sessions/14-ansible/ex2-galaxy-ansible.md

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

curl https://gist.githubusercontent.com/raonyguimaraes/e70220921504d26a0627050ade17bc24/raw/327f952683dc550613c4c60b2b74d32427dde0ea/galaxy_ansible_install.sh | sh

$ 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 SlidesExercise (E)(G)
10:20 Extending installation SlidesExercise (G)
10:40 Defining and importing genomes, Data Managers SlidesExercise (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/