Galaxy Conference – Admin 25/06/2018

Galaxy Release Schedule

3 releases per year: January, May and September

Install Galaxy using Ansible

sudo pip install ansible
git clone
cd GalaxyKickStart
git checkout 2018-gccbosc
ansible-galaxy install -r requirements_roles.yml -p roles –force

curl | 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:

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

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

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.

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.

$ planemo test –no-container –engine toil seqtk_seq.cwl


planemo o

#this will open the browser

cd /srv/galaxy/server/lib/galaxy/jobs/runners


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

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). -->
 <plugin id="local" type="runner" load="" workers="4"/>
 <destination id="local" runner="local"/>


      - rule_type: file_size
        lower_bound: 16
        upper_bound: Infinity
        destination: slurm-2c
    default_destination: slurm_cluster
default_destination: local_no_container
verbose: True


attach 28376



Raony Guimaraes