Nextstrain_instructions/Installation at main · CoVaRR-NET/Nextstrain_instructions · GitHub

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#Instructions for installing nextstrain on a cc cluster (tested on narval)
#Clone the ncov repository
git clone https://github.com/nextstrain/ncov

#create virtual environment called nextstrain
module load python
virtualenv --no-download nextstrain
#activate the nextstrain environment
source nextstrain/bin/activate

#install nextstrain and dependencies
pip install nextstrain-augur==13.0.0
pip install epiweeks==2.1.2
curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextalign-Linux-x86_64" -o "nextalign" && chmod +x nextalign
#install Pangolin
git clone https://github.com/edluffy/pangolin
cd pangolin
pip3 install -r requirements.txt
cd ../
#install PangoLEARN
git clone https://github.com/cov-lineages/pangoLEARN.git
cd pangoLEARN
python setup.py install
cd ../

#the pre-installed treetime module doesn't work, so clone:
git clone https://github.com/neherlab/treetime.git
cd treetime
pip install .
cd ../

#install more dependancies:
pip install nextstrain-cli
pip install boto3 #get error that it had to uninstall botocor-1.23.24 and instead installs version 1.23.37 ontop
pip install snakemake
pip install Bio #get ERROR: nextstrain-augur 13.0.0 has requirement biopython<=1.76,>=1.67, but you'll have biopython 1.79+computecanada which is incompatible.
#but still installs successfully

#didn't run these:
pip install treetime #<- why do we need this? isn't it installed above?
pip install pyQt5 #doesn't install, says requirements are already satisfied in lib/python3.8/site-packages in computecanada
#note: pyQt5 installs above with pangolin

#load cc modules
module load gcc mafft iq-tree raxml fasttree vcftools scipy-stack

#ensure that everything is in the path
export PATH="/project/ctb-bourqueg-ab/genfs/projects/COVID_covarrnet/susanne_sandbox:$PATH"

#check the setup
nextstrain check-setup --set-default
#the checkup will fail, but snakemake and augur should be listed as installed

#test your installation, this test dataset should run through without any errors if everything is correctly installed
#note: ensure that cc modules are loaded (e.g. needs iqTree) and also set path to the nextstrain folder where everything is installed
cd ncov
#go into defaults and add row 'Wuhan/WIV04/2019' to file 'include.txt' to always include our reference
snakemake --profile my_profiles/getting_started/ -p

#this last command should do a full run (make an alignment and build a divergence tree with iqTree and a time tree with TreeTime, results saved inside ncov folder)