Name: usegalaxy-playbook
Owner: Galaxy Project
Description: Ansible Playbook for usegalaxy.org
Created: 2014-09-03 20:51:31.0
Updated: 2018-01-10 18:42:40.0
Pushed: 2017-12-01 18:19:14.0
Homepage: null
Size: 6861
Language: Python
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
This Ansible playbook is used to deploy and maintain the public Galaxy servers, namely Galaxy Main (usegalaxy.org) and Galaxy Test (test.galaxyproject.org). The generalized roles herein have been
published to Ansible Galaxy and can be installed for your own use via the ansible-galaxy command, but
a few site-specific roles are contained here as well.
This playbook is not designed to be used by Galaxy deployers/admins at other sites, but should be useful as a reference for anyone wishing to emulate a setup like usegalaxy.org.
Usage documentation can be found in the usegalaxy-playbook wiki.
You will need the vault password to run most plays. These can be found in the galaxyproject pass(1) password store. If you have configured a gpg-agent(1), you can pipe pass directly to ansible-playbook like so:
ss ansible/vault/usegalaxy | ansible-playbook --vault-password-file=/bin/cat [additional options...]
A handy shell function to run the common playbooks with pass can be found in the wiki.
Tools are installed using the roles/galaxyproject.tools role. Each
Galaxy instance has the toolset to be installed listed under
files/galaxy/test.galaxyproject.org|usegalaxy.org/tool_list.yaml so edit that
file to include new tools or versions. An admin user API key is required to
install the tools, and it is stored in the Vault under api_key variable.
Run the role with (replace stage with production for Main):
% ansible-playbook tools.yml --ask-vault-pass -i stage/inventory
Note that by default this roll will create a virtualenv in your /tmp dir. The
installation log is available in /tmp/galaxy_tool_install.log.
Building Pulsar's dependencies' dependencies as an unprivileged user on some HPC systems was a difficult manual process, so I made some notes, which may be helpful:
slurm-drmaa compiled and installed by hand on Stampede (slurm-devel is not installed (or worse, some login nodes have mismatched versions), so I had to work around this):
cd slurm
mkdir -p include/slurm
cd src/slurm-2.6.3
./configure --prefix=/usr
cp slurm/*.h ../../include/slurm
cd slurm-drmaa-1.0.7
./configure --prefix=/work/galaxy/test/slurm-drmaa --with-slurm-inc=/work/galaxy/test/slurm/include && make && make install
Python + virtualenv compiled and installed by hand on Stampede:
cd /work/galaxy/test/python/src/Python-2.7.6
./configure --prefix=/work/galaxy/test/python --enable-unicode=ucs4 && make && make install
cd ../virtualenv-1.11.5
/work/galaxy/test/python/bin/python setup.py install
Prior to conda integration there was no good way to install dependencies for Pulsar. What I'd done for those dependencies was:
rsync the tool_dependency_dir from the Galaxy server to the Pulsar server.
Use find and sed to alter paths in env.sh
Recreate virtualenvs in deps using {{ instance_root }}/python/bin/virtualenv venv,
but this requires removing include/python2.7, lib/python2.7, and copying
site-packages from the old venv to the new venv. Obviously not a sustainable model.
Academic Free License (“AFL”) v. 3.0