Overview

The CernVM-FS is a distributed filesystem perfectly designed for sharing readonly data across the globe. We use it in the Galaxy Project for sharing things that a lot of Galaxy servers need. Namely:

• Reference Data
  • Genome sequences for hundreds of useful species.
  • Indices for the genome sequences
  • Various bioinformatic tool indices for the available genomes
• Tool containers
  • Singularity containers of everything stored in Biocontainers (A bioinformatic tool container repository.) You get these for free every time you build a Bioconda recipe/package for a tool.
• Others too..

From the Cern website:

The CernVM File System provides a scalable, reliable and low-maintenance software distribution service. It was developed to assist High Energy Physics (HEP) collaborations to deploy software on the worldwide-distributed computing infrastructure used to run data processing applications. CernVM-FS is implemented as a POSIX read-only file system in user space (a FUSE module). Files and directories are hosted on standard web servers and mounted in the universal namespace /cvmfs.”

A slideshow presentation on this subject is available. More details are available on usegalaxy.org (Galaxy Main’s) reference data setup and CVMFS system.

This exercise describes a manual process to install and configure CVMFS and Galaxy’s access to CVMFS. For a tutorial that uses Ansible to perform these tasks, see the Reference Data with CVMFS tutorial.

Agenda

1. Overview
2. CVMFS and Galaxy without Ansible
   1. Configuring CVMFS
   2. Testing it out
   3. Look at the repository

CVMFS and Galaxy without Ansible

Comment: Manual version of Ansible Commands

If you wish to perform the same thing that we’ve just done, but by building the ansible script manually, follow these instructions. Otherwise, you have already done everything below and do not need to re-do it.

We are going to setup a CVMFS mount to the Galaxy reference data repository on our machines. To do this we have to install and configure the CVMFS client and then mount the appropriate CVMFS repository using the publicly available keys.

Hands-on: Installing the CVMFS Client

1. On your remote machine, we need to first install the Cern software apt repo and then the CVMFS client and config utility:

   sudo apt install lsb-release
   wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb
   sudo dpkg -i cvmfs-release-latest_all.deb
   rm -f cvmfs-release-latest_all.deb
   sudo apt-get update
   
   sudo apt install cvmfs cvmfs-config
   

2. Now we need to run the CVMFS setup script.

   sudo cvmfs_config setup
   

Configuring CVMFS

The configuration is not complex for CVMFS:

Hands-on: Configuring CVMFS

1. Create a /etc/cvmfs/default.local file with the following contents:

   CVMFS_REPOSITORIES="data.galaxyproject.org"
   CVMFS_HTTP_PROXY="DIRECT"
   CVMFS_QUOTA_LIMIT="500"
   CVMFS_CACHE_BASE="/srv/cvmfs/cache"
   CVMFS_USE_GEOAPI=yes
   

   This tells CVMFS to mount the Galaxy reference data repository and use a specific location for the cache which is limited to 500MB in size and to use the instance’s geo-location to choose the best CVMFS repo server to connect to. You can use the cvmfs_quota_limit role variable to control this setting.

Tip: What is a good size for CVMFS_QUOTA_LIMIT?

In production UseGalaxy.org.au uses 100GB, different sites have different needs and you can make your cache smaller depending on your usage. E.g. if your users only use one dataset from the reference data (e.g. just hg38) then perhaps you don’t need such a large cache.

1. Create a /etc/cvmfs/domain.d/galaxyproject.org.conf file with the following contents:

   CVMFS_SERVER_URL="http://cvmfs1-tacc0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-iu0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-psu0.galaxyproject.org/cvmfs/@fqrn@;http://galaxy.jrc.ec.europa.eu:8008/cvmfs/@fqrn@;http://cvmfs1-mel0.gvl.org.au/cvmfs/@fqrn@;http://cvmfs1-ufr0.galaxyproject.eu/cvmfs/@fqrn@"
   

   This is a list of the available stratum 1 servers that have this repo.

2. Create a /etc/cvmfs/keys/data.galaxyproject.org.pub file with the following contents:

   -----BEGIN PUBLIC KEY-----
   MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA5LHQuKWzcX5iBbCGsXGt
   6CRi9+a9cKZG4UlX/lJukEJ+3dSxVDWJs88PSdLk+E25494oU56hB8YeVq+W8AQE
   3LWx2K2ruRjEAI2o8sRgs/IbafjZ7cBuERzqj3Tn5qUIBFoKUMWMSIiWTQe2Sfnj
   GzfDoswr5TTk7aH/FIXUjLnLGGCOzPtUC244IhHARzu86bWYxQJUw0/kZl5wVGcH
   maSgr39h1xPst0Vx1keJ95AH0wqxPbCcyBGtF1L6HQlLidmoIDqcCQpLsGJJEoOs
   NVNhhcb66OJHah5ppI1N3cZehdaKyr1XcF9eedwLFTvuiwTn6qMmttT/tHX7rcxT
   owIDAQAB
   -----END PUBLIC KEY-----
   

3. Make a directory for the cache files

   sudo mkdir /srv/cvmfs
   

Testing it out

Probe the connection.

Hands-on: Testing it out

1. Run sudo cvmfs_config probe data.galaxyproject.org

   Question

   What does it output?

   Solution

   OK
   

   If this doesn’t return OK then you may need to restart autofs: sudo systemctl restart autofs

2. Change directory into /cvmfs/ and list the files in that folder

   Question

   What do you see?

   Solution

   You should see nothing, as CVMFS uses autofs in order to mount paths only upon request.

3. Change directory into /cvmfs/data.galaxyproject.org/.

   Input: Bash

   cd /cvmfs/data.galaxyproject.org/
   ls
   ls byhand
   ls managed
   

   Question

   What do you see now?

   Solution

   You’ll see .loc files, genomes and indices. AutoFS only mounts the files when they’re accessed, so it appears like there is no folder there.

   And just like that we all have access to all the reference genomes and associated tool indices thanks to the Galaxy Project, IDC, and Nate’s hard work!

   Tip: Contributing Reference Genomes

   If you are developing a new tool, and want to add a reference genome, we recommend you talk to us on Gitter. You can also look at one of the tools that uses reference data, and try and copy from that. If you’re developing the location files completely new, you need to write the data manager.

Look at the repository

Now to configure Galaxy to use the CVMFS references we have just installed, see the Ansible tutorial.

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Citing this Tutorial

1. Simon Gladman, Helena Rasche, Reference Data with CVMFS without Ansible (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/cvmfs-manual/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{admin-cvmfs-manual,
author = "Simon Gladman and Helena Rasche",
	title = "Reference Data with CVMFS without Ansible (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/cvmfs-manual/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs-manual/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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