Setup Robin

Kraken2

download https://github.com/DerrickWood/kraken2.git (either git repo or just the files, repo is recommended because of updates) ./install_kraken2.sh build #make sure you are in kraken2 folder cp build/kraken2{,-build,-inspect} ../bin #or manually create resources/bin folder and copy paste build/kraken2-build, kraken2-inspect

more information: https://github.com/DerrickWood/kraken2/wiki/Manual

downloading their databases: https://benlangmead.github.io/aws-indexes/k2

Downloading the human reference genome: wget -P resources https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40/download?include_annotation_type=GENOME_FASTA&include_annotation_type=GENOME_GFF&include_annotation_type=RNA_FASTA&include_annotation_type=CDS_FASTA&include_annotation_type=PROT_FASTA&include_annotation_type=SEQUENCE_REPORT&hydrated=FULLY_HYDRATED

mv "download?include_annotation_type=GENOME_FASTA" GRCh38_data.zip

Creating a screen session for background tasks:

How to use GNU Screen

Start a new screen session

screen -S mysession

(Replace 'mysession' with any name you like.)

Detach from the current screen session

Press:

Ctrl+a d

(Hold Ctrl, press 'a', release both, then press 'd'.)

List all screen sessions

screen -ls

Reattach to a screen session

screen -r mysession

(Or use the session ID from 'screen -ls'.)

Kill a screen session

First, reattach and type 'exit' or press Ctrl+d,

or from outside any session:

screen -S mysession -X quit

(Replace 'mysession' with your session name or ID.)

"Lab"book: created a snakemake test in the screen: snakemake_test

unzip GRCh38_data.zip -d GRCh38_data

For some reason you need to write the command like this: snakemake --cores all --use-conda --conda-frontend conda

It's important that conda-forge is above bioconda in the envs