Background and external resources
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bash Miniconda3-latest-Linux-x86_64.sh |
Install sra-tools
Once conda is installed in the instance. Go to https://anaconda.org and search for sra-tools. Copy and paste the command to install the tool in your HPC account:
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conda install -c bioconda sra-tools |
Download SRA filesSubmit
a Example: PBS script (launch_fetch_SRAfiles.pbs) to fetch multiple files from SRA filesdatabase
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#!/bin/bash -l #PBS -N SRAfiles #PBS -l walltime=2:00:00 #PBS -l mem=4gb #PBS -l ncpus=2 #PBS -m bae ###PBS -M email@host #PBS -j oe cd $PBS_O_WORKDIR ### User defined SRA identifiers SRAIDACCESSIONS=SRR1002659,SRR1002660,SRR1002661,SRR1002662 ### Pipeline #Step1: Download SRA file prefetch ${SRAIDACCESSIONS} #Step2: Extract FASTQ file(s) from SRA file fastq-dump --split-files ${SRAID}ACCESSIONS} |
submit PBS script to the HPC cluster
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qsub launch_fetch_SRAfiles.pbs |
monitor job progression
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qjobs |