Installation

On CSC Roihu: No Installation Needed

LazypipeX is published as a dataset project on at the (CSC). The dataset carries the pipeline, its complete toolchain and all reference databases, and is readable by every user with a CSC account:

   module use /dataset/project_2020379/modulefiles
   module load lazypipe/3.1

Both lines are required — module load lazypipe on its own will report that the module does not exist. Do not load other tool modules on top of lazypipe; the modulefile already provides every dependency at the version the databases were built against.

The dataset project supplies files only: it has no compute allocation and no writable space. Run jobs from your own CSC project and bill them there.

Full guide: . For many samples at once, see .

On Any Other Linux Cluster

Up-to-date installation instructions are maintained with the code, in the :

• — overview and quick start
• — directory setup, dependencies, Perl modules, R libraries, reference databases, host filters, and the bundled test suite

In outline:

git clone
cd LazypipeX 
conda create -n blast   -c bioconda blast 
conda create -n lazypipe -c bioconda -c eclarke bwa csvtk fastp krona megahit mga minimap2 "samtools>=1.12" seqkit spades taxonkit trimmomatic numpy scipy requests 
make test        # tiers 0-1: no databases needed, ~30 s

Reference databases and host/background genomes are installed separately with perl/install_db.pl; see the user guide for the current list and the disk space each requires. Verify the result with make test-all.

Notes:

• Samtools must be 1.12 or newer — LazypipeX uses the samtools view -e filter expressions introduced in that release.
• Reserve at least 4 GB of RAM per core.
• Working files need roughly ten times the size of the compressed FASTQ input; put them on fast local disk where possible.

 Earlier Versions

Lazypipe 1–3 remain available at the . The CSC Puhti module described in the older has been retired along with Puhti; on CSC systems, use the Roihu dataset module above.

See Also