Due to Aspera license limitations, users have to install the software under their home to user the software.
For example, for user abc123, the working directory will be
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srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -n 1 /bin/bash
mkdir /n/scratch3/users/${USER:0:1}/${USER}/testDbGaP
cd /n/scratch3/users/${USER:0:1}/${USER}/testDbGaP
module load sratoolkit/2.10.7 |
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# Configure sratoolkit
vdb-config --interactive
# Directly press x key to quit
# By default, sratoolkit uses working diretory as cache. It is better to use scratch3 instead:
echo /repository/user/main/public/root = \"/n/scratch3/users/${USER:0:1}/${USER}/ncbi\" >> ~/.ncbi/user-settings.mkfg
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# Upload the dbGaP repository Key to O2:
scp ~/Download/prj_phs710EA_test.ngc $USER@transfer.rc.hms.harvard.edu:~/.ncbi
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# Load sratookit module
module load sratoolkit/2.10.7
# Use prefetch to download SRA file.
prefetch --ngc ~/.ncbi/prj_phs710EA_test.ngc -p SRR1219902
# Convert SRA file to FASTQ with fastq-dump. -X 5 means only gives first five reads to give a quick test.
fastq-dump -X 5 --ngc ~/.ncbi/prj_phs710EA_test.ngc --split-files SRR1219902
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