...
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mkdir $HOME/data/myProjectName/ |
Now Example: now you are ready to download the Fastq.gz files
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bs download project -i 357263934 -o $HOME/data/myProjectName/ --extension=fastq.gz |
Download files using a PBS Pro script (i.e., called launch_fetch_BaseSpaceData.pbs):
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#!/bin/bash -l
#PBS -N fetchBaseSpace
#PBS -l walltime=24:00:00
#PBS -l mem=32gb
#PBS -l ncpus=8
#PBS -m bae
###PBS -M email@host
#PBS -j oe
cd $PBS_O_WORKDIR
#fetch data from BaseSpace by indicating the Project ID (-i parameter)
bs download project -i 357263934 -o /my/project/raw_data --extension=fastq.gz
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Submit the job to the PBS Pro scheduler (queue):
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qsub launch_fetch_BaseSpaceData.pbs |
Monitor progress:
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qjobs |
It can take ~15-20 min to download ~170GB of data.