Difference between revisions of "SRA"
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and change the directory to, for example, /ufrc/$GROUP/$USER/ncbi/public. See the [https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration SRA Toolkit Configuration Documentation] for more details. | and change the directory to, for example, /ufrc/$GROUP/$USER/ncbi/public. See the [https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration SRA Toolkit Configuration Documentation] for more details. | ||
| + | Alternatively, create an 'ncbi' directory in your /ufrc space and symlink it to ~/ncbi. E.g. | ||
| + | |||
| + | $ mkdir /ufrc/mygroup/$USER/ncbi | ||
| + | $ ln -s /ufrc/mygroup/$USER/ncbi ~/ncbi | ||
<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
Revision as of 18:10, 6 June 2018
Description
This is the NCBI Short Read Archive Toolkit.
- Note
- sra will create a $HOME/ncib/public directory and cache the prefetched data files there. However, home directory has a 20gb limit and its use for job data storage is a violation of the UFRC storage policy. You must change that location to a directory in your ufrc space before running the sra toolkit. The official approach is to use the vdb-config tool
vdb-config -i
and change the directory to, for example, /ufrc/$GROUP/$USER/ncbi/public. See the SRA Toolkit Configuration Documentation for more details.
Alternatively, create an 'ncbi' directory in your /ufrc space and symlink it to ~/ncbi. E.g.
$ mkdir /ufrc/mygroup/$USER/ncbi $ ln -s /ufrc/mygroup/$USER/ncbi ~/ncbi
Required Modules
Serial
- sra
System Variables
- HPC_{{#uppercase:sra}}_DIR - installation directory
- HPC_SRA_BIN - location of the executables directory
- HPC_SRA_DOC - location of the documentation directory
Additional Information
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:
ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa
will download the all.faa.tar.gz archive to the faa directory.
Note: if the download fails to run with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error please submit a support request. This means that the remote site has not been allowed through the firewall. Please be sure to include the command you used when filing your request.