Installation

Installation

seqcounter needs Python 3.10 or newer and BBTools, which provides seal.sh and needs Java. seqcounter itself has no Python dependency: it uses only the standard library.

conda (recommended)

BBTools is not on PyPI, so the simplest route is a conda environment holding both:

conda create -n seqcounter -c conda-forge -c bioconda bbmap python">=3.10"
conda activate seqcounter
pip install seqcounter
seqcounter --version

mamba or micromamba work the same way and are faster.

pip, with BBTools already installed

pip install seqcounter

or, without touching your environment:

pipx install seqcounter

seal.sh must be in your PATH. seqcounter also finds a seal.sh installed next to the Python that runs it, so /path/to/env/bin/seqcounter works without activating that environment.

To install BBTools by hand instead, download it from SourceForge, unpack it and add its folder to your PATH:

tar -xzf BBMap_39.13.tar.gz
export PATH="$PWD/bbmap:$PATH"
seal.sh --version

From a clone

Nothing has to be installed to run seqcounter from a clone, as the first version did:

conda create -n seqcounter -y -c conda-forge -c bioconda bbmap python">=3.10"
conda activate seqcounter
git clone https://github.com/duceppemo/seqcounter
cd seqcounter
python seqcounter.py -h

python seqcounter.py takes exactly the same arguments as the installed seqcounter command, so scripts written for the first version keep working. pip install -e . from the clone adds the seqcounter command as well.

Checking the installation

bash examples/run_example.sh

from a clone generates a reference file and four samples whose counts are known, counts them and prints the reports. Without a clone:

printf '>ref1\nTTCGAACGCTGACGTCAGCATCGATTGCAGCTAGCTTAGCGATCGGATCGA\n' > refs.fasta
seqcounter -ref refs.fasta -r1 refs.fasta -o test_out   # ref1 is found once, in its own file

Which version is installed

seqcounter --version
seal.sh --version          # BBTools and Java

The JSON report of every run also records the versions of seqcounter, Python, BBTools and Java that produced it.