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Your Home directory contains the genomic data and other data resources. It accessed by clicking the 'Home' application on the desktop. You can also access your home directly through the 'terminal' application. 

Home directory structure

The Home directory can be accessed via the Home icon on the desktop.

You home directory inside the research environment desktop has a hard limit of 10GB. Exceeding this limit will render you unable to log in to the environment. You will then need to raise a ticket in order for space to be freed up so that you can log in again.

We provide a large shared working space for all users depending on the type of user. For all academic researchers, this will be a folder in re_gecip. For discovery forum members, this will be a folder in discovery_forum.

You home directory on the HPC environment is seperate to the home directory in the research environment desktop, and is also more relaxed in the amount of space that you can use. We do, however, recommend using the shared folders described above.

 In your home directory there are links to a number of important folders. These folders are:

FolderIconReadWriteDesktop PathMounted on HPCHPC PathDescription

(tick)(error)~/genomes(tick)/genomesAll the genomic data provided by our sequence partner Illumina (see Genomic Data from Illumina).

(tick)(error)~/gel_data_resources(tick)/gel_data_resourcesOutputs from the Genomics England internal pipelines (see Genomics England Data).

(tick)(error)~/public_data_resources(tick)/public_data_resourcesPublic data resources such as 1,000 genomes data, reference genomes, example scripts etc (see Public data resources).
specific shared folder

(tick)(tick)~/<group_name>(tick)/<group_name>Backed-up working space for each group (e.g. re_gecip). There are several petabytes of storage space for use and collaboration.

The genomes, gel_data_resources, and public_data_resources folders are read-only, whilst the specific group shared folder is read-write and the ideal place to store all your work.

(warning) All of these folders are also mounted on the HPC at root ( / ) so you can access them when running programs on the HPC. Your home folder in the Research Environment desktop is NOT available on the HPC. Please use the specific group share instead. 

If you attempt to write anything to genomes, gel_data_resources or public_data_resources you will get a 'permission denied' error. Please note that this will happen if an attempt is made to gunzip a file with no output directory specified. Consider using the following command instead: gunzip -c file_name > /path/to/output.file

GeCIP Shared Working Space

If you are a member of GeCIP, you will be able to read and write to the 're_gecip' folder. Use this folder as your working space. Within this folder, are sub-folders categorised by GeCIP domain (e.g. neurology, cardiovascular, skin, etc). In the Research Environment, you will be able to 'see' all of these sub-folders, however you will only have read-write access to the sub-folders that you are a member of. The re_gecip folder is mounted on the HPC, so any files and folders you save here, will be accessible from the HPC. We recommend saving all your work to your domain folder within the re_gecip folder as you have much more storage allocation. How you organise the domains shared working space is entirely up to you!  

Discovery Forum Shared Working Space

Each Discovery Forum group will have their own specific shared folder which should be used as the shared working space. This folder has several petabytes of storage available and is mounted on the HPC at root ( / ). The folder has restricted access to each particular Discovery Forum member. 

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