ELIXIR-Italy CVMFS documentation

ELIXIR-Italy maintain two CVMFS repository, exploited by Laniakea.

CVMFS

Flavours supported

folder tree

elixir-italy.covacs.refdata

galaxy CoVaCS

tree structure

elixir-italy.galaxy.refdata

galaxy Epigen, galaxy RNA-workbench, Galaxy GDC Somatic Variant Calling

tree structure

A complete list of the reference data, with download link, is available here.

Default folders structure

The basic structure of the CVMFS repositories is the same. The repository directories are referred to the model organism genome different assemblies:

  • at10

  • at9

  • dm2

  • dm3

  • dm6

  • hg18

  • hg19

  • hg38

  • mm10

  • mm8

  • mm9

  • sacCer1

  • sacCer2

  • sacCer3

Inside each assembly directory there is the genome.fa and the refseq gtf and gff downloaded from UCSC and the tools indeces:

bwa

It has been created using the default command

$ bwa index -a bwtsw genome.fa

bowtie2

It has been created using the default command

$ bowtie2-build

bowtie

Created using the default command

$ bowtie-build

rsem

Created using the default command

$ rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) <assembly-name>

Additional folders

The two repositories hosts also spceific directories:

elixir-italy.covacs.refdata

annovar_db

Hosts the databases needed to perform CoVaCS pipeline downloaded from annovar repository using the annotate_variation.pl perl script.

bed_file_covacs

Hosts the bed files needed to perform CoVacs pipeline, the same bed files were present in the CINECA implementation of the CoVaCS pipeline.

location

Hosts the .loc file and the tool_data_table.xml file that will be used by galaxy CoVaCS flavours.

elixir-italy.galaxy.refdata

rRNAdatabase

Location of ribosomial RNA for sortmeRNA tool in galaxy RNA workbench flavour.

index_GATK_bundle

Location of genome indices for GATK toools for hg38 and hg19 assembly downloaded from GATK ftp bundle (https://software.broadinstitute.org/gatk/download/bundle).

location

Hosts the .loc file and the tool_data_table.xml file that will be used by galaxy RNA workbench, galaxy EPIGEN and galaxy GDC Somatic Variant flavours

CVMFS server details

Since, cvmfs relies on OverlayFS or AUFS as default storage driver and Ubuntu 16.04 natively supports OverlayFS, it is used as default choice to create and populate the cvmfs server.

A resign script is located in /usr/local/bin/Cvmfs-stratum0-resign and the corresponding weekly cron job is set to /etc/cron.d/cvmfs_server_resign.

Log file is located in /var/log/Cvmfs-stratum0-resign.log.