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