HIER

Section: CCB Directory Hierarchy (7)
Last updated: Wed 10 Jan 16:53:42 GMT 2024
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DEPRECATION NOTICE

This CCB documentation has been superseded by our new website: https://lumin.imm.ox.ac.uk

OVERVIEW

This page describes the file hierarchy on the JADE cluster. At a high level, the various file locations are available across the whole cluster and you can read and write data from anywhere. /ceph is the root mount of our primary data store and the place you should store most of your data. A number of sub-locations within this are available via symbolic links described below.

KEY SYMBOLIC LINKS

The / (root) filesystem on the CCB cluster contains a number of symbolic links which you can use to refer to other data locations. We recommend using these rather than the absolute file paths where possible, as we reserve the right to change the location of data where necessary but will endeavor to ensure that the links always point to the correct target.

/databank - A link to /ceph/databank/ and the location for reference genomes. See igenomes(7) for further details.

/home/[a-z] - A set of links to /ceph/home/[a-z] and the locations of home directories.

/miseq - A link to /ceph/miseq and the location where new NGS data is uploaded. See miseq(7) for further details.

/project - A link to /ceph/project/ and the location for collaboration projects. See project(7) for further details.

/package - A link to /ceph/package/OS_VERSION which contains the computational biology software which is provided through the module system. See modules(7) for further details.

DIFFERENCES FROM T1-DATA

The CCB historically used storage referred to as t1-data which is now retired. For long-time CCB users, there are some key differences:

- There are no users quotas for the Ceph; all quotas are per-project

- File paths which previously started /t1-data no longer work

- All data is stored in 3 copies at 2 separate physical locations for resilience; there are no separate backups and the old /t1-data backups have been switched off

- The Ceph has a special feature which removes the need to use the du(1) command. To find out how much data a directory contains, use a command in the form

ls -ldh DIRNAME

substituting DIRNAME for the directory in question. Please be aware that this total may take an hour or two to update when data is added or removed

GETTING HELP

You can email the CCB team using the email address help@imm.ox.ac.uk. Using this address ensures your email is logged and assigned a tracking number, and will go to all the core team, which means the appropriate person or people will be able to pick it up.

COPYRIGHT

This text is copyright University of Oxford and MRC and may not be reproduced or redistributed without permission.

AUTHOR

Duncan Tooke <duncan.tooke@imm.ox.ac.uk>