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software:topical:lifescience:sra

The NCBI SRA (Sequence Read Archive)

The SRA toolkit is a collection of tools for using data in the INSDC Sequence Read Archives.

Documentation

Using the toolkit is documented in a comprehensive handbook.

Modules on Mogon

The toolkit is available as a module:

bio/SRA-Toolkit/<version/build>

Loading just bio/SRA-Toolkit will load the most recent version.

We highly recommend choosing a version >= 2.10 due to the simpler configuration management, which in parts is incompatible with version lower than this.

Choosing the Storage Path(s)

Among other possible configuration settings, the SRA toolkit lets you choose the storage path, where so-called dumps will store their files:

$ vdb-config --interactive

will open an interactive dialogue, where you can choose the so-called location of user-repository in the CACHE tab.

This user repository can either be in your $HOME or your projects path. As the stored amount of data can reach considerable space and particularly this can be considered a project's shared data, we recommend choosing the project path. This be any one of:

  • On Mogon I select /project/<project-name>/<optional sub-path>.
  • On Mogon II select /lustre/project/<project-name>/<optional sub-path> or a project path in the scratch file system.

Users with projects on both systems may change this setting at any time.

Also, vdb-config lets you set the download path for prefetched files: in the TOOLS tab you can select either your home directory or the current directory. For the same two reasons as for the prefetch path, we recommend selecting the current working directory and to navigate to the actual project prior to the dumping command.

software/topical/lifescience/sra.txt · Last modified: 2020/02/12 08:30 by meesters