- recipe seq2squiggle
End-to-end simulation of nanopore sequencing signals with feed-forward transformers
- Homepage:
- License:
MIT
- Recipe:
- package seq2squiggle¶
- versions:
0.3.0-0- depends appdirs:
>=1.4.4,<2.0.0- depends lightning:
>=2.2.5,<3.0.0- depends matplotlib-base:
>=3.9.0,<4.0.0- depends numba:
>=0.59.0,<0.60.0- depends numpy:
>=1.26.4,<2.0.0- depends ont_vbz_hdf_plugin:
>=1.0.1- depends pod5:
>=0.3.12,<0.4.0- depends prettytable:
>=3.9.0,<4.0.0- depends pygithub:
>=2.3.0,<3.0.0- depends pysam:
>=0.22.0,<0.23.0- depends pyslow5:
>=1.1.0,<2.0.0- depends python:
>=3.10.0,<4.0.0- depends pytorch:
>=2.3.1,<3.0.0- depends pyyaml:
>=6.0.1,<7.0.0- depends rich-click:
>=1.8.2,<2.0.0- depends scikit-learn:
>=1.4.0,<2.0.0- depends tqdm:
>=4.66.2,<5.0.0- depends transformers:
>=4.41.2,<5.0.0- depends wandb:
>=0.16.3,<0.17.0- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install seq2squiggle and update with:: mamba update seq2squiggle
To create a new environment, run:
mamba create --name myenvname seq2squiggle
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/seq2squiggle:<tag> (see `seq2squiggle/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/seq2squiggle/README.html)
