[CVMFS] Improve Laniakea CVMFS (elixir-italy.galaxy.refdata)

[mtangaro]

Improve the CVMFS repository, replacing elixir-italy.galaxy.refdata, with more storage (at leaste 2 TB).

• Add squid proxy by default!
• Move all reference data here, dropping from Laniakea past implementations. [DONE]
• Add vinyl reference datasets. [DONE]

[mtangaro]

A new repository have been created: data.elixir-italy-cvmfs. Please follow this tutorial to move to this new repository.

[mtangaro]

The old ELIXIR-Italy reference-data repository is mounted to /cvmfs/elixir-italy.covacs.refdata.

1. First of all log into your Galaxy instance through SSH using your favourite application. Please have a look here how to do:

   • for MacOS and Linux
   • fow Windows

2. Turn off Galaxy:

   sudo supervisorctl stop galaxy:

   please note the : symbol after the galaxy word.

3. Umount the old repository:

   sudo cvmfs_config umount elixir-italy.covacs.refdata

   To check if the command has been correctly run check with the command df -h that the repository elixir-italy.covacs.refdata IS NOT in the ouptut list.

4. Remove the old configuration:

   sudo rm /etc/cvmfs/config.d/elixir-italy.covacs.refdata.conf
   sudo rm /etc/cvmfs/keys/elixir-italy.covacs.refdata.pub

5. Install the new repository configuration:

   • download and install the configuration file:

     
     cd /etc/cvmfs/config.d

sudo wget https://raw.githubusercontent.com/indigo-dc/Reference-data-galaxycloud-repository/master/cvmfs_server_config_files/data.elixir-italy-cvmfs.conf

- download and install the key:

cd /etc/cvmfs/keys/

sudo wget https://raw.githubusercontent.com/indigo-dc/Reference-data-galaxycloud-repository/master/cvmfs_server_keys/data.elixir-italy-cvmfs.pub

- Configure the repository:

sudo cvmfs_config probe data.elixir-italy-cvmfs Probing /cvmfs/data.elixir-italy-cvmfs... OK

You can check the repository is correctly installed listing the attached volumes with "df -h". The CVMFS repository entry should be there 

$ df -h Filesystem Size Used Avail Use% Mounted on /dev/vda1 20G 5.2G 15G 26% / devtmpfs 1.9G 0 1.9G 0% /dev tmpfs 1.9G 4.0K 1.9G 1% /dev/shm tmpfs 1.9G 17M 1.9G 1% /run tmpfs 1.9G 0 1.9G 0% /sys/fs/cgroup /dev/vdb1 47G 650M 44G 2% /export tmpfs 379M 0 379M 0% /run/user/4002 tmpfs 379M 0 379M 0% /run/user/4001 tmpfs 379M 0 379M 0% /run/user/0 cvmfs2 4.0G 9.1M 3.9G 1% /cvmfs/data.elixir-italy-cvmfs

6. Edit Galaxy configuration

cd /home/galaxy/galaxy/config/

mv tool_data_table_conf.xml tool_data_table_conf.xml.old

wget https://raw.githubusercontent.com/indigo-dc/Reference-data-galaxycloud-repository/master/data.elixir-italy-cvmfs/location/tool_data_table_conf.xml

7. Then restart Galaxy:

sudo supervisorctl restart galaxy:

again please note the ```:``` symbol after ```galaxy```.