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00_SetUp.md

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Bacterial WGS training : Exercise 0

|**Title**| Working environment setup.| |---------|-------------------------------------------| |**Training dataset:**| |**Questions:**|
  • How do I install the software for the course?
  • Where do I get the data for the exercises?
| |**Objectives**:|
  • In this document we will cover the working environment setup for the exercises.
| |**Time estimation**:| 5 min | |**Key points**:|
  • Each practical is designed to work on this [folder structure](#final-folder-structure), so make sure you follow these steps correctly.
|
#### IMPORTANT: Make sure you understand and execute these commands in the right order.

Open a new terminal and navigate to your home directory if you are not already there:

pwd
cd
pwd

Create the project folder for the practises of the course:

mkdir -p Documents/wgs

Navigate to the directory:

cd Documents/wgs

Download git repository:

git clone https://github.com/BU-ISCIII/bacterial_wgs_training.git

Download training dataset:

wget https://github.com/BU-ISCIII/bacterial_wgs_training/releases/download/1.0/training_dataset.tar.gz
tar -xvzf training_dataset.tar.gz
rm -f training_dataset.tar.gz

Get the container (singularity image) by the method which suits you the most:

If you are taking the course in one of our virtual machines, the fastest way to do it is by copying it from the shared folder:

rsync ~/course_shared_folder/wgs_bacterial.simg ./

The second option is to download it from our dockerhub:

singularity pull docker://buisciii/bacterial_wgs_training

The last option (only for advanced users) is to build the image from the recipe inside the repository you just cloned. You may need to execute it as root and edit images permissions to work under your user:

singularity build wgs_bacterial.simg bacterial_wgs_training/Singularity
Final folder structure
.
├── bacterial_wgs_training
│   ├── bin
│   │   └── plotTreeHeatmap.R
│   ├── conf
│   │   ├── base.config
│   │   ├── docker.config
│   │   ├── multiqc_config.yaml
│   │   └── singularity.config
│   ├── config2.file
│   ├── config.file
│   ├── Dockerfile
│   ├── exercises
│   │   ├── 00_SetUp.md
│   │   ├── 01_LinuxNextflowSingularity.md
│   │   ├── 02_QualityAndAssembly.md
│   │   ├── 03_outbreakSNP.md
│   │   ├── 04_outbreakcgMLST
│   │   └── img
│   │       ├── Ex_2_1.png
│   │       ├── Ex_2_2.png
│   │       ├── itol_web1.png
│   │       ├── itol_web2.png
│   │       ├── tree_with_bad_sample_snps.png
│   │       └── tree_with_bad_sample_snps.svg
│   ├── main.nf
│   ├── nextflow.config
│   ├── README.md
│   ├── scif_app_recipes
│   ├── Singularity
│   └── slides
│       └── talk1
│           └── PITCHME.md
├── training_dataset
│   ├── ARGannot.r1.fasta
│   ├── downsampling_250K
│   │   ├── RA-L2073_R1.fastq.gz
│   │   ├── RA-L2073_R2.fastq.gz
│   │   ├── RA-L2281_R1.fastq.gz
│   │   ├── RA-L2281_R2.fastq.gz
│   │   ├── RA-L2327_R1.fastq.gz
│   │   ├── RA-L2327_R2.fastq.gz
│   │   ├── RA-L2391_R1.fastq.gz
│   │   ├── RA-L2391_R2.fastq.gz
│   │   ├── RA-L2450_R1.fastq.gz
│   │   ├── RA-L2450_R2.fastq.gz
│   │   ├── RA-L2677_R1.fastq.gz
│   │   ├── RA-L2677_R2.fastq.gz
│   │   ├── RA-L2701_R1.fastq.gz
│   │   ├── RA-L2701_R2.fastq.gz
│   │   ├── RA-L2709_R1.fastq.gz
│   │   ├── RA-L2709_R2.fastq.gz
│   │   ├── RA-L2782_R1.fastq.gz
│   │   ├── RA-L2782_R2.fastq.gz
│   │   ├── RA-L2805_R1.fastq.gz
│   │   ├── RA-L2805_R2.fastq.gz
│   │   ├── RA-L2978_R1.fastq.gz
│   │   └── RA-L2978_R2.fastq.gz
│   ├── listeria_NC_021827.1_NoPhagues.fna
│   ├── listeria_NC_021827.1_NoPhagues.gff
│   ├── pcr_serogroup_listeria.fas
│   └── pcr_serogroup_listeria.scheme
└── wgs_bacterial.simg