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.
Start by cloning Lazypipe repository:
git clone https://plyusnin@bitbucket.org/plyusnin/lazypipe.git
cd lazypipe
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 $(pwd)/SANSPANZ.3/runsanspanz.py ~/bin/runsanspanz.py
Install modules to local-lib ~/perl5
cpan --local-lib=~/perl5 File::Basename File::Temp Getopt::Long YAML::Tiny
export PERL5LIB=~/perl5/lib/perl5:$PERL5LIB
Open R console and type
install.packages( c("reshape","openxlsx") );
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.
URL | Local path (config.yaml) | Installation | Description |
---|---|---|---|
NA |
blastp_db |
See NCBI manual | NCBI BLAST nr database |
blastn_vi_db_url | blastn_vi_db | perl/install_db.pl --db blastn_vi | NCBI GeneBank Viruses Complete genomes |
fairdata link | centrifuge_db | download and unpack data/nt_2021_12_habv_cent.tar.gz |
centrifuge index with Hsapiens_GRCh38p13 assembly + bacteria + archaea + virus sequences from NCBI nt database |
fairdata link | minimap_db | download and unpack data/2022_11_04.nt_abv.tar.gz | Archaeal, bacterial and virus sequences from NCBI nt database |
taxonomy_url | taxonomy | perl/install_db.pl --db taxonomy | NCBI Taxonomy database |
Table 1. Summary on databases used by Lazypipe.
You are now all set up. To test Perl interface type:
perl lazypipe.pl
To test Snakemake interface type:
snakemake -np all
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.