ELIXIR-Italy CVMFS documentation ================================ ELIXIR-Italy maintain two CVMFS repository, exploited by Laniakea. .. csv-table:: :header: "CVMFS", "Flavours supported", "folder tree" :widths: auto :file: table_cvmfs.csv 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: .. hlist:: :columns: 2 - 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 .. code:: bash $ bwa index -a bwtsw genome.fa ----------- ``bowtie2`` ----------- It has been created using the default command .. code:: bash $ bowtie2-build ---------- ``bowtie`` ---------- Created using the default command .. code:: bash $ bowtie-build -------- ``rsem`` -------- Created using the default command .. code:: bash $ rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) 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``.