Installation

This guide provides detailed instructions how to set up ClusTRace on Puhti server (CSC). Installing on other unix serveres follows similar steps.

Start by cloning the repository

git clone https://plyusnin@bitbucket.org/plyusnin/clustrace.git

Install bioinformatic tools

Tool CSC module Website Direct download Original article
IQ-TREE 2 NA http://www.iqtree.org/ linux 64-bit https://doi.org/10.1093/molbev/msaa015
MAFFT v7 biokit https://mafft.cbrc.jp/alignment/software/ linux 64-bit https://doi.org/10.1093/molbev/mst010
MsaToVcf NA http://lindenb.github.io/jvarkit/MsaToVcf.html NA https://doi.org/10.1099/mgen.0.000056
Pangolin bioconda https://cov-lineages.org/resources/pangolin.html NA https://doi.org/10.1093/ve/veab064
SeqKit NA https://bioinf.shenwei.me/seqkit/ linux 64-bit https://doi.org/10.1371/journal.pone.0163962
snpEff NA http://pcingola.github.io/SnpEff/ NA https://doi.org/10.4161/fly.19695
TreeCluster NA https://github.com/niemasd/TreeCluster NA https://doi.org/10.1371/journal.pone.0221068
Trimal biokit http://trimal.cgenomics.org/ linux 64-bit https://doi.org/10.1093/bioinformatics/btp348
VeryFastTree NA https://github.com/citiususc/veryfasttree NA https://doi.org/10.1093/bioinformatics/btaa582

Hint: you do not need to install all tools, just those that you intend to use (e.g. IQ-Tree2 or VeryFastTree).

Install Perl Modules

module load biokit # run on CSC to load correct Perl env
cpanm --local-lib=~/perl5 Bio::SeqIO Bio::TreeIO Clone Excel::Writer::XLSX File::Basename File::Temp Getopt::Long Sort::Naturally Struct::Dumb Time::Piece
#add this line to your ~/.bashrc file
export PERL5LIB=~/perl5/lib/perl5

For more information please see https://bitbucket.org/plyusnin/clustrace/src/master/