CSC module

Lazypipe is available as a preinstalled module on Puhti server at the Finnish Center of Scientific Computing (CSC).

For usage instuctions please refer to the CSC documentation.

Note: we recommend to reserve at least 4GB of RAM for each core when running Lazypipe.

How to install lazypipe

Clone the repository

Start by cloning Lazypipe repository:

git clone https://plyusnin@bitbucket.org/plyusnin/lazypipe.git
cd lazypipe

Install Binaries with Conda

conda create -n blast -c bioconda blast
conda create -n lazypipe -c bioconda -c eclarke bwa centrifuge csvtk fastp krona megahit mga minimap2 samtools seqkit spades snakemake-minimal taxonkit trimmomatic numpy scipy fastcluster requests

Or from conda yaml files (before calling change the "name" and "prefix" to match your conda installation):

conda env create -f blast.yml
conda env create -f lazypipe.yml

This will create separate conda environment for blast. All other tools are installed under lazypipe. To activate all installed binaries type:

conda activate blast
conda activate --stack lazypipe

Set taxonomy database location for KronaGraph (you may need to replace $CONDA_PREFIX and $data according to your settings):

rm -rf $CONDA_PREFIX/conda/env/lazypipe/opt/krona/taxonomy

ln -s $data/taxonomy $CONDA_PREFIX/conda/env/lazypipe/opt/krona/taxonomy

Set env variable $TM to point to trimmomatic directory:

export TM=$CONDA_PREFIX/share/trimmomatic

Download PANNZER (version 02/2022 or later) and set runsanspanz.py as executable to your path:

wget http://ekhidna2.biocenter.helsinki.fi/sanspanz/SANSPANZ.3.tar.gz
tar -zxvf SANSPANZ.3.tar.gz
sed -i "1 i #!$(which python)" SANSPANZ.3/runsanspanz.py
ln -sf $(pwd)/SANSPANZ.3/runsanspanz.py ~/bin/runsanspanz.py

Install Perl modules

Install modules to local-lib ~/perl5

cpan --local-lib=~/perl5 File::Basename File::Temp Getopt::Long YAML::Tiny
export PERL5LIB=~/perl5/lib/perl5:$PERL5LIB

Install R libraries

Open R console and type

install.packages( c("reshape","openxlsx") );

Install local databases

Open config.yaml and set local paths for taxonomy, blastp_db, blastn_vi_db and minimap_db.

Start by installing NCBI taxonomy database:

perl perl/install_db.pl --db taxonomy

Then install blastn_vi_db database:

perl perl/install_db.pl --db blastn_vi

To use Lazypipe annotations with minimap2, download and unpack the latest NCBI nt archaea+bacteria+viruses (link in Table 1).

To use Lazypipe with Centrifuge, download and unpack your preferred Centrifuge index.

Table 1. Summary on databases used by Lazypipe.

Test Perl and Snakemake interfaces

You are now all set up. To test Perl interface type:

perl lazypipe.pl

To test Snakemake interface type:

snakemake -np all

Complete list of Lazypipe dependencies

Table 2. Lazypipe dependencies. Tools in square brackets mark binaries that are not required for basic Lazypipe runs. When installed, these will provide additional options/functionalities.