Page Comparison

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• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )

• Basic unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

• Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

Download the data from BaseSpace

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mkdir $HOME/data/myProjectName/

Now Example: now you are ready to download the Fastq.gz files

 bs download project -i-name 357263934 -o $HOME/data/myProjectName/ --extension=fastq.gz

Download files using a PBS Pro script (i.e., called launch_fetch_BaseSpaceData.pbs):

#!/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 --name 357263934 -o /my/project/raw_data --extension=fastq.gz

Submit the job to the PBS Pro scheduler (queue):

qsub launch_fetch_BaseSpaceData.pbs

Monitor progress:

qjobs

It can take ~15-20 min to download ~170GB of data.