- recipe modifi
DNA modification detection from PacBio SMRT metagenomic data
- Homepage:
- License:
MIT / MIT
- Recipe:
MODIFI detects DNA base modifications and infers host-mobile genetic element (MGE) linkages from PacBio metagenomic sequencing data. It supports modification calling, motif discovery, and host-MGE association for both subreads and HiFi read types. Native motif finding uses pbmotifmaker (from pbtk) on Linux if installed; otherwise use the bundled MultiMotifMaker.jar (OpenJDK). On macOS, install PacBio tools separately or rely on the JAR fallback.
- package modifi¶
- Versions:
0.0.3-0,0.0.1-0- Depends:
on adjusttext
on bash
on biopython
on h5py
on joblib
on libgcc
>=14on libstdcxx
>=14on matplotlib-base
on numpy
on openjdk
on pandas
on pbmm2
on pbtk
on psutil
on pysam
on pyyaml
on regex
on samtools
on scikit-learn
on scipy
on seaborn
on statsmodels
on tqdm
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install modifi
to add into an existing workspace instead, run:
pixi add modifi
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install modifi
Alternatively, to install into a new environment, run:
conda create -n envname modifi
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/modifi:<tag>
(see modifi/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/modifi/README.html)
