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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):
Download the data from BaseSpace
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bs download project -i-name 357263934 -o $HOME/data/myProjectName/ --extension=fastq.gz |
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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#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 --iname 357263934 -o /my/project/raw_data --extension=fastq.gz |
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