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sratoolkit/2.10.7 to download dbGAP data
sratoolkit/2.10.7 to download dbGAP data
- Lingsheng Dong
- Neil Coplan
Owned by Lingsheng Dong
Due to Aspera license limitations, users have to install the software under their home to user the software.
Start interactive job, and create working folder and load sratoolkit modue
For example, for user abc123, the working directory will be
srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -n 1 /bin/bash
mkdir /n/scratch/users/${USER:0:1}/${USER}/testDbGaP
cd /n/scratch/users/${USER:0:1}/${USER}/testDbGaP
module load sratoolkit/2.10.7Configure sratoolkit. Only need to do this once:
# Configure sratoolkit
vdb-config --interactive
# Directly press x key to quit
# By default, sratoolkit uses working diretory as cache. It is better to use scratch instead:
echo /repository/user/main/public/root = \"/n/scratch/users/${USER:0:1}/${USER}/ncbi\" >> ~/.ncbi/user-settings.mkfg
Downoading dbGaP repository Key and upload to O2:
# Upload the dbGaP repository Key to O2:
scp ~/Download/prj_phs710EA_test.ngc $USER@transfer.rc.hms.harvard.edu:~/.ncbi
Use sratoolkit prefetch, which try ascp then http, to download sra data, then convert the data from .sra to .fastq format
, multiple selections available,
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