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    Installing SingleM

    There are several ways to install SingleM. On the assumption that a standard internet connection speed is available, each of these methods should take substantially less than 1 hour, hopefully less than 15 minutes.

    SingleM can be installed through Bioconda. Lyrebird is installed by installing SingleM, and then using the lyrebird command instead of singlem e.g. use lyrebird pipe ... instead of singlem pipe ....

    conda create -c bioconda -c conda-forge --name singlem singlem'>='0.19.0

    Test if it works by running

    conda activate singlem
singlem -h
lyrebird -h

    After this, you'll also need to procure the reference data (the "metapackage"). See singlem data or lyrebird data.

    Installation via DockerHub

    A docker image generated from the conda package is available on DockerHub. After installing Docker, run the following:

    docker pull wwood/singlem:0.19.0

    Test if it works by running

    docker run wwood/singlem:0.19.0 -h

    If the sequence data to be analyzed is in the current working directory, SingleM pipe can be used like so:

    docker run -v `pwd`:`pwd` wwood/singlem:0.19.0 pipe --sequences \
    `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4

    Two things to note:

    1. The default SingleM reference data is included in the docker image, so running singlem data is not necessary for this installation method - you can jump straight to using pipe.
    2. You should not specify singlem in the command line, as this is automatic. Simply use e.g. docker run wwood/singlem:0.19.0 pipe -h.

    A similar procedure is true for Lyrebird, except that the docker image is different, so you need to run:

    docker pull wwood/lyrebird:0.19.0
docker run wwood/lyrebird:0.19.0 -h

    Installation via Singularity / Apptainer

    SingleM can be installed via Singularity or Apptainer. After installing Singularity or Apptainer, run the following:

    singularity pull docker://wwood/singlem:0.19.0

    Test if it works by running

    singularity run singlem_0.19.0.sif -h

    If the sequence data to be analyzed is in the current working directory, SingleM pipe can be used like so:

    singularity run -B `pwd`:`pwd` singlem_0.19.0.sif pipe --sequences \
    `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4

    Two things to note:

    1. The default SingleM reference data is included in the docker image, so running singlem data is not necessary for this installation method - you can jump straight to using pipe.
    2. You should not specify singlem in the command line, as this is automatic. Simply use e.g. singularity run singlem_0.19.0.sif pipe -h.

    A similar procedure is true for Lyrebird, except that the docker image is different, so you need to run:

    singularity pull docker://wwood/lyrebird:0.19.0
singularity run -B `pwd`:`pwd` lyrebird_0.19.0.sif -h

    Installation via PyPI

    To install the Python libraries required for SingleM / Lyrebird:

    pip install singlem

    You may need super-user privileges.

    SingleM also has several non-Python dependencies, which are documented in the pixi.toml file in the base directory of the repository. You'll also need to procure the reference data (the "metapackage"). See singlem data.

    Installation via Github, with pixi dependency management

    SingleM can be installed from source together with its conda dependencies as follows. You will need to have pixi installed first.

    git clone https://github.com/wwood/singlem
cd singlem
pixi shell

singlem -h
lyrebird -h

    After this, you'll also need to procure the reference data (the "metapackage"). See singlem data.

    This prcedure also installs lyrebird, but the reference metapackage is different. See lyrebird data for more information.

    Example data

    To test the main subcommand of SingleM, pipe works, download a minimal dataset and generate a taxonomic profile like so:

    wget 'https://github.com/wwood/singlem/raw/44e1f81404c12931742259088999290edbb271b3/test/data/methanobacteria/genomes/GCA_000309865.1_genomic.fna'
singlem pipe -1 GCA_000309865.1_genomic.fna -p /dev/stdout

    This should output a profile similar to the below. When tested, the pipe took a little less than 2 minutes:

    sample  coverage        taxonomy
GCA_000309865.1_genomic 0.39    Root; d__Archaea; p__Methanobacteriota; c__Methanobacteria; o__Methanobacteriales; f__Methanobacteriaceae; g__Methanobacterium
08/06/2024 04:50:25 PM INFO: Finished condense

    Containerised SingleM installation examples

    To ensure that the instructions here work, they have been tested in containerised environments. Logs of this procedure are available at https://github.com/wwood/singlem-installation.

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