Installation

Installation

Requirements: Python ≥ 3.10 and Mash 2.3. mashID has no Python dependencies.

bioconda (recommended)

conda create -n mashID -c conda-forge -c bioconda mashid
conda activate mashID
mashID -h

Mash is pulled in as a dependency, so this is the only step. Add python-isal to the environment to make gzip decompression two to three times faster when counting reads; it is optional.

Three commands are installed: mashID, make_mashID_db and mashID_download_db.

conda + pip

To install a version that is not on bioconda yet:

conda create -n mashID -c conda-forge -c bioconda python=3.12 pip mash=2.3 python-isal
conda activate mashID
pip install https://github.com/duceppemo/mashID/archive/refs/tags/v0.3.2.tar.gz
mashID -h

From a clone

git clone https://github.com/duceppemo/mashID
cd mashID
conda env create -f environment.yml
conda activate mashID
pip install .

Running from the source tree without installing also works: python mashID.py -h.

Adding mashID to an existing environment

conda install -c conda-forge -c bioconda mashid

The package is named mashid in lowercase; both mashID and mashid work as commands.

Verify the installation

The repository ships a small synthetic example with its own database and expected results, so nothing needs to be downloaded:

git clone https://github.com/duceppemo/mashID && cd mashID   # if not already cloned
bash example/run_example.sh

It screens four samples (paired-end reads, a mixed culture, an assembly, and an unrelated sequence) and reports OK when the summary matches example/expected/summary_mashID.tsv. The Example page walks through the results.

Databases

No database is bundled. Download the default one (286.9 MB, sketch and sidecars) after installing:

mashID_download_db mycobacteriaceae

See Databases for the other pre-built databases and how to build your own.

Troubleshooting

mash: error while loading shared libraries: libgsl.so.25 The solver picked an older bioconda build of Mash 2.3 linked against GSL 2.6/2.7. Request the current build, which links against GSL 2.8:

conda install -c conda-forge -c bioconda "mash=2.3=*_11"

The 'mash' executable was not found on PATH Activate the conda environment that contains Mash, or install it: conda install -c bioconda mash.

No database given and the default 'mycobacteriaceae' database is not installed Run mashID_download_db mycobacteriaceae, or pass -d /path/to/your.msh.