Due to the large size of the resource files, I recommend downloading only those required for your annotations:
Java class WGSA085.class and folders javaclass, hg19 and hg38 under resources are required for any annotations.
Folder precomputed and precomputed_hg38 is recommended for speeding up gene-model based annotation for large-scale SNP data in hg19 and hg38, respectively. To use them, set gene-model annotation on the fly in setting file as either i or n.
The corresponding folders for other resources can be found in the resource list file.
Use any preferred software to download the folders.
Example batch download command for creating the resources folder and downloading javaclass, hg19, and hg38 to it:
mkdir resources
cd resources
wget http://web.corral.tacc.utexas.edu/WGSAdownload/resources/javaclass/ --recursive --continue --timestamping --no-host-directories --cut-dirs=2 --no-parent --reject="index.html*"
wget http://web.corral.tacc.utexas.edu/WGSAdownload/resources/hg19/ --recursive --continue --timestamping --no-host-directories --cut-dirs=2 --no-parent --reject="index.html*"
wget http://web.corral.tacc.utexas.edu/WGSAdownload/resources/hg38/ --recursive --continue --timestamping --no-host-directories --cut-dirs=2 --no-parent --reject="index.html*"
Example batch download command for downloading the full WGSA076 pipeline (1.5 Tb) to WGSA:
mkdir WGSA
cd WGSA
wget http://web.corral.tacc.utexas.edu/WGSAdownload/ --recursive --continue --timestamping --no-host-directories --cut-dirs=1 --no-parent --reject="index.html*"