There are several ways to install SingleM.
SingleM can be installed through Bioconda:
conda create -c bioconda -c conda-forge --name singlem singlem'>='0.17.0
Test if it works by running
conda activate singlem
singlem -h
After this, you'll also need to procure the reference data (the "metapackage"). See singlem data.
A docker image generated from the conda package is available on DockerHub. After installing Docker, run the following:
docker pull wwood/singlem:0.17.0
Test if it works by running
docker run wwood/singlem:0.17.0 -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:0.17.0 pipe --sequences \
`pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
Two things to note:
pipe
.singlem
in the command line, as this is automatic. Simply use e.g. docker run wwood/singlem:0.17.0 pipe -h
.SingleM can be installed via Singularity or Apptainer. After installing Singularity or Apptainer, run the following:
singularity pull docker://wwood/singlem:0.17.0
Test if it works by running
singularity run singlem_0.17.0.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_0.17.0.sif pipe --sequences \
`pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
Two things to note:
pipe
.singlem
in the command line, as this is automatic. Simply use e.g. singularity run singlem_0.17.0.sif pipe -h
.To install the Python libraries required:
pip install singlem
You may need super-user privileges.
SingleM also has several non-Python dependencies, which are documented in the singlem.yml
file in the base directory of the repository. You'll also need to procure the reference data (the "metapackage"). See singlem data.
SingleM can be installed from source together with its conda dependencies as follows.
git clone https://github.com/wwood/singlem
cd singlem
conda env create -n singlem -f singlem.yml
conda activate singlem
cd bin
export PATH=$PWD:$PATH
singlem -h
After this, you'll also need to procure the reference data (the "metapackage"). See singlem data.
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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