course_install.txt

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-Linux-x86_64.sh

rm Miniconda3-latest-Linux-x86_64.sh

conda config --add channels defaults; conda config --add channels bioconda; conda config --add channels conda-forge; conda config --set channel_priority strict

conda install mamba -n base -c conda-forge

mamba init

#restart shell after installing mamba

mamba create -n qc fastq-scan=1.0.0 fastqc=0.11.9 fastp=0.23.2 kraken2=2.1.2 bracken=2.7 multiqc=1.13a

mamba install pandas -n qc -c conda-forge 

mamba create -n mapping bwa=0.7.17 samtools=1.15 bcftools=1.14 pysam=0.16.0.1 biopython=1.78

mamba install pandas -n qc -c conda-forge 

mamba create -n shovill shovill=1.1.0

#update below command in the setup

mamba create -n quast quast=5.2.0

mamba create -n bakta bakta=1.6.1

mamba create -n nextflow nextflow

mamba create -n phylogenetics snp-sites=2.5.1 iqtree=2.2.0.3

mamba create -n mlst mlst=2.22.1

mamba create -n seroba seroba=1.0.2

mamba create -n spoligotyping spotyping=2.1

mamba create -n tbprofiler tb-profiler=4.1.1

mamba create -n ariba ariba=2.14.6

mamba create -n artemis -c bioconda artemis

mamba create -n figtree -c bioconda figtree

mamba create -n prokka -c bioconda prokka

mv bact_gen_workshop2023 workshop_files_Bact_Genomics_2023