waldronlab/sratoolkit repository overview

Built at https://hub.docker.com/repository/docker/waldronlab/sratoolkit⁠

Try (from here⁠):

For all runs of this sample use runs="SRR2244401;SRR2236793;SRR2243639;SRR2243812;SRR2244215;SRR2245587;SRR2228273;SRR2228283;SRR2228304;SRR2228308;SRR2228313;SRR2228320;SRR2228347;SRR2228399;SRR2226903;SRR2226948;SRR2227815;SRR2228028;SRR2228363;SRR2228450;SRR2228455;SRR2228709"

sample="M1.1.SA"
runs="SRR2244401;SRR2236793"
mkdir reads
fastq-dump --outdir reads ${runs}
echo 'Downloaded.'
echo 'Concatenating runs...'
cat reads/*.fastq > reads/${sample}.fastq
ls -l reads/