Build kb-python reference for GENCODE release M26 GRCm39

build_kbref_Gencode_release26_GRCm39

## This is only on compute canada clusters where modules are available!
module load python/3.7.4

## Create virtual environment using python
python3 -m venv ./kb_python_env

## activate environment
source ./kb_python_env/bin/activate

## Install kb-python inside environment
pip3 install kb-python

## Download references from Gencode
mkdir references
cd ./references
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/GRCm39.primary_assembly.genome.fa.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M26/gencode.vM26.annotation.gtf.gz

cd ..
kb ref --workflow standard -i ./references/kb_ref.GRCm39.idx -g ./references/t2g_kb_ref.GRCm39.txt -f1 ./references/cdna.GRCm39 ./references/GRCm39.primary_assembly.genome.fa.gz ./references/gencode.vM26.annotation.gtf.g