Metadata-Version: 2.1
Name: loreme
Version: 0.1.0
Summary: Extract Methylation calls from ONT or PB long read data
Author-email: Anthony Aylward <aaylward@salk.edu>
Project-URL: Homepage, https://gitlab.com/salk-tm/loreme
Project-URL: Documentation, https://salk-tm.gitlab.io/loreme
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: urllib3
Requires-Dist: pybedtools
Requires-Dist: gff2bed
Requires-Dist: seaborn
Requires-Dist: pyfaidx
Requires-Dist: psutil
Requires-Dist: gputil
Requires-Dist: tabulate
Requires-Dist: nvsmi
Requires-Dist: pod5

# LoReMe pipeline

TODO: make a 'loreme clean' subcommand to remove downloads before uninstalling

Analysis of CpG methylation calls from PacBio HiFi or ONT data. See also the [full documentation](https://salk-tm.gitlab.io/loreme/index.html)

Other tools of interest: [methylartist](https://github.com/adamewing/methylartist) and [modbamtools](https://github.com/rrazaghi/modbamtools)  ([modbamtools docs](https://rrazaghi.github.io/modbamtools/)), [methplotlib](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214038/)

## Installation

### Conda

The recommended way to install `loreme` is with a dedicated `conda` environment:

First create an environment including all dependencies:
```
conda create -n loreme -c conda-forge -c bioconda pbmm2 urllib3 \
  pybedtools gff2bed seaborn pyfaidx psutil gputil tabulate \
  cython h5py iso8601 more-itertools polars tqdm
conda activate loreme
```

Then install with `pip`:
```
pip install loreme
```

Alternatively, install from the git repo:
```
git clone https://gitlab.com/salk-tm/loreme.git
cd loreme
pip install .
```

You may also wish to install `nvtop` to monitor GPU usage:
```
conda install -c conda-forge nvtop
```

### Check installation

Check that the correct version was installed with `loreme --version`
