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Storage description

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  1. Storage description
    1. Description Filesystems
    2. Good practices
    3. Quick links

Before using the current MIB infrastructure it is good practice to have some info about the storage available.

Several available partitions are shared among all users with no quota per user. Every user is responsible of his data and should use the storage according to the good practices rules described here.

Description Filesystems

The blue color for a box means that the filesystem (FS) is not available from the compute nodes.

The green color for a box means that the filesystem (FS) is accessible from the compute nodes.

Use the command df -h or lsblk /dev/sda to list filesystem and their size.

/seq

backup?: Not yet

Open to users?: No

Available on compute nodes?: No

Description:

  • Raw sequencing files should be stored here.
  • Only admins can write in this folder.
  • Users can read all files present. If you receive new sequencing data contact the local admin to add it here.

/projects

backup?: Not yet

Open to users?: Yes, in specific folder only

Available on compute nodes?: No

Description:

  • This folder will contain all users project file.
  • Users can manage their own folders.
  • All users can read all files

/homemib

backup?: Not yet

Open to users?: Yes, in specific folder only

Available on compute nodes?: Yes

Description:

  • This folder contains home folders of all mib users. Each user manages their own home folder.
  • Use your home folder to store files other than genomic data. Documents, scripts...

/home

backup?: Not yet

Open to users?: Yes, in specific folder only

Available on compute nodes?: No

Description:

  • This folder contains home folders of all micevo users.

/work

backup?: No

Open to users?: Yes

Available on compute nodes?: Yes

Description:

  • This folder should be used to run analyses. Input data may be read from a different filesystem but the output should always be in this partition.
  • Every user can make a folder to work in. Users are responsible for removing their output folders when analyses are done.

/tools

backup?: No

Open to users?: Yes

Available on compute nodes?: Yes

Description:

  • Most of bioinformatics software will be installed here. But please use the mechanism described in Submitting jobs to know how to load and use those programs.

  • Test data will also be available here. If you develop software or script please make small test data available here for all users.
  • All users except guests and students have write permissions in all folders here. If you do create a folder in here please make sure to set writing rights to group.

Not active yet

backup?: No

Open to users?: Yes

Available on compute nodes?: Local to compute nodes, each node has it's own scratch folder

Description:

  • Automatically created

Good practices

Coming soon

  • Keep work folder clean
  • Keep home folder clean
  • Always have data in /seq
  • From /work to /projects

  1. Computers description

  2. Request an account

  3. storage description

  4. First login

  5. Receiving sequencing data

  6. transferring data

  7. Submitting jobs

  8. Monitor jobs

  9. Install tools

  10. Space management

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