SRA-Toolkit on Helix
The NCBI SRA SDK generates loading and dumping tools with their respective libraries for building new and accessing existing runs.
There are multiple versions of the SRA-Toolkit available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail sratoolkit
To select a module, type
module load sratoolkit/[ver]
where [ver] is the version of choice.
If you are using the SRA Toolkit for the first time, you will need to set up a local repository directory.
For versions 2.3 and above, you will need an X11 connection. Type:
java -jar $SRATOOLKITHOME/preview/sratoolkit.jar
and follow the directions for setting up a local repository.
For versions earlier than 2.3, type:
configuration-assistant.perl
and again follow the directions.
In both cases, DO NOT choose your /home directory, as it does not have enough space to hold SRA files.
Configuration will create a directory ~/.ncbi that holds configuration information about your local SRA repository, as well as the repository directory itself.
Example
GUI access:
java -jar $SRATOOLKITHOME/preview/sratoolkit.jar
Command-line access:
module load sratoolkit fastq-dump SRR390728 sam-dump SRR390728 > SRR390728.sam
