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CVMFS-Client_tutorial.md

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How to connect to a CVMFS repository.

The Cern-VM file system (CVMFS).

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 everytime 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." - https://cernvm.cern.ch/portal/filesystem

CVMFS and Galaxy

The Galaxy project supports a few CVMFS repositories.

Repository Repository Address Contents
Reference Data and Indices data.galaxyproject.org Genome sequences and their tool indices, Galaxy .loc files for them as well
Singularity Containers singularity.galaxyproject.org Singularity containers for everything in Biocontainers for use in Galaxy systems
Galaxy Main Configuration main.galaxyproject.org The configuration files etc for Galaxy Main (usegalaxy.org)

Setting up an instance to access a CVMFS repository

You will be provided with the ip address of an instance running in the NeCTAR Cloud. It will be running Ubuntu 16.04.

See here for a list of the available machines.

We are going to log into them via ssh and setup a CVMFS mount to the Galaxy reference data repository as an example.

The images are pretty vanilla, they only have vim and nano installed outside of the standard NeCTAR Ubuntu image.

Step 1: Install the CVMFS client

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

Now we need to run the cvmfs setup script.

sudo cvmfs_config setup

Step 2: Create some config files and a directory

default.local

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

CVMFS_REPOSITORIES="data.galaxyproject.org"
CVMFS_HTTP_PROXY="DIRECT"
CVMFS_QUOTA_LIMIT="32000"
CVMFS_CACHE_BASE="/mnt/galaxyIndices/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 32GB in size and to use the instance's location to choose the best CVMFS repo server to connect to.

galaxyproject.org.conf

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

CVMFS_SERVER_URL="http://cvmfs1-psu0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-iu0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-tacc0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-mel0.gvl.org.au/cvmfs/@fqrn@"

This is a list of the available tier1 servers that have this repo. Note there is one in Melbourne. We will most likely be connecting to this one.

data.galaxyproject.org.pub

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-----

galaxyIndices

Make a directory for the cache files

sudo mkdir /mnt/galaxyIndices

Step 3: Check to see if it is working

Probe the connection.

sudo cvmfs_config probe data.galaxyproject.org

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

Step 4: Look at the repository

Go and take a look in /cvmfs/data.galaxyproject.org. You will see the contents of the repo. There is quite a lot of data here all available and ready to go..

Just like that....