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Add Linux lesson 1
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@pvanheus
pvanheus committed Mar 4, 2024
1 parent efd7a01 commit 2073d81
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Showing 30 changed files with 19,359 additions and 61 deletions.
20 changes: 20 additions & 0 deletions data/shell/file_list1.csv
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SRR8364252,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364252_1.fastq.gz
SRR8364252,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364252_2.fastq.gz
SRR8364253,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364253_1.fastq.gz
SRR8364253,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364253_2.fastq.gz
SRR8364254,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364254_1.fastq.gz
SRR8364254,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364254_2.fastq.gz
SRR8364255,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364255_1.fastq.gz
SRR8364255,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364255_2.fastq.gz
SRR8364256,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364256_1.fastq.gz
SRR8364256,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364256_2.fastq.gz
SRR8364257,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364257_1.fastq.gz
SRR8364257,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364257_2.fastq.gz
SRR8364258,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364258_1.fastq.gz
SRR8364258,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364258_2.fastq.gz
SRR8364259,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364259_1.fastq.gz
SRR8364259,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364259_2.fastq.gz
SRR8364260,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364260_1.fastq.gz
SRR8364260,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364260_2.fastq.gz
SRR8364261,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364261_1.fastq.gz
SRR8364261,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364261_2.fastq.gz
20 changes: 20 additions & 0 deletions data/shell/file_list2.csv
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SRR8364252,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364252_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364252_2.fastq.gz
SRR8364252,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364252_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364252_2.fastq.gz
SRR8364253,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364253_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364253_2.fastq.gz
SRR8364253,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364253_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364253_2.fastq.gz
SRR8364254,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364254_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364254_2.fastq.gz
SRR8364254,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364254_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364254_2.fastq.gz
SRR8364255,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364255_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364255_2.fastq.gz
SRR8364255,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364255_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364255_2.fastq.gz
SRR8364256,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364256_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364256_2.fastq.gz
SRR8364256,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364256_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364256_2.fastq.gz
SRR8364257,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364257_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364257_2.fastq.gz
SRR8364257,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364257_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364257_2.fastq.gz
SRR8364258,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364258_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364258_2.fastq.gz
SRR8364258,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364258_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364258_2.fastq.gz
SRR8364259,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364259_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364259_2.fastq.gz
SRR8364259,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364259_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364259_2.fastq.gz
SRR8364260,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364260_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364260_2.fastq.gz
SRR8364260,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364260_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364260_2.fastq.gz
SRR8364261,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364261_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364261_2.fastq.gz
SRR8364261,https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364261_1.fastq.gz;https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads/SRR8364261_2.fastq.gz
Empty file modified data/shell/make_case_data.py
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8 changes: 8 additions & 0 deletions data/shell/make_file_list1.sh
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#!/bin/bash

url=https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads

for file in $(ls reads/) ; do
sample=${file%*_[12].fastq.gz}
echo $sample,${url}/$file
done
8 changes: 8 additions & 0 deletions data/shell/make_file_list2.sh
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#!/bin/bash

url=https://pathogen-genomics-march-2024.sanbi.ac.za/data/shell/reads

for file in $(ls reads/) ; do
sample=${file%*_[12].fastq.gz}
echo $sample,${url}/${sample}_1.fastq.gz\;${url}/${sample}_2.fastq.gz
done
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