SRA¶

Description¶

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

The toolkit contains loading and dumping tools with their respective libraries for building new and accessing existing runs.

The online documentation is located at https://github.com/ncbi/sra-tools/wiki

Environment Modules¶

Run module spider sra to find out what environment modules are available for this application.

Environment Variables¶

HPC_SRA_DIR - location of the installation directory
HPC_SRA_BIN - location of the executables directory
HPC_SRA_DOC - location of the documentation directory

Additional Usage Information¶

Warning

The sra toolkit creates a $HOME/ncbi/public directory for caching prefetched data files. Home directory has a 40gb limit and its use for job data storage is a violation of the RC storage policy.

Please change the location to a directory in your /blue directory tree before running the sra toolkit. The official approach is to use the vdb-config tool

vdb-config -i

In the config tool change the directory to, for example, /blue/$GROUP/$USER/ncbi/public. See the SRA Toolkit Configuration Documentation for more details.

Alternatively, use a symlink to redirect the cache directory to blue.

Remove the ncbi directory in your home directory:
```
    $ cd
    $ rm -rf ncbi
```
Create a ncb directory in your /blue space
```
    $ mkdir /blue/mygroup/$USER/ncbi
```
Symlink the ncbi directory in /blue into your /home directory
```
    $ ln -s /blue/mygroup/$USER/ncbi/ ~/ncbi
```

Uploads¶

It appears that data uploads to NCBI only work from login servers because of likely IP address range blocks. Start a screen session before beginning an upload if there are any concerns about being disconnected.

Aspera Connect¶

To download SRA data you can use the "ascp" utility from the Aspera Connect browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ascp.sh that automatically uses the ssh key is available.

For instance, the following command will download the all.faa.tar.gz archive to the faa directory:

ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa

Note: if the download fails to run with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error make sure you are running aspera connect on a login node. If you are already doing the transfer on a login node please submit a support request. This means that the remote site has not been allowed through the firewall. Please be sure to include the path to a script you used to run the data transfer command into the request. Do not put any sensitive information like passwords, keys, and such into the request.

Categories¶

biology, ngs