Package Recipe 'dram'

recipe dram

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Homepage:: https://github.com/shafferm/DRAM/
Documentation:: https://github.com/shafferm/DRAM/wiki
License:: GPL / GPL-3.0
Recipe:: /dram/meta.yaml
Links:: doi: 10.1101/2020.06.29.177501

package dram¶

Versions:

1.5.0-0, 1.4.6-2, 1.4.6-1, 1.4.6-0, 1.4.5-0, 1.4.3-0, 1.4.2-0, 1.4.1-0, 1.4.0-0,

1.5.0-0, 1.4.6-2, 1.4.6-1, 1.4.6-0, 1.4.5-0, 1.4.3-0, 1.4.2-0, 1.4.1-0, 1.4.0-0, 1.3.5-0, 1.3.4-0, 1.3.3-0, 1.3.2-0, 1.3-0, 1.2.4-1, 1.2.4-0, 1.2.2-0, 1.2.1-0, 1.2.0-0, 1.1.1-0, 1.1.0-0, 1.0.6-0

Depends:

on altair >=4
on barrnap
on curl
on hmmer
on mmseqs2 >10.6d92c
on networkx
on numpy
on openpyxl
on pandas >=1.5,<2
on parallel
on prodigal
on python >=3.8
on ruby
on scikit-bio >=0.5.8,<0.6
on scipy >=1.9
on sqlalchemy
on trnascan-se >=2
on wget

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 dram

to add into an existing workspace instead, run:

pixi add dram

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 dram

Alternatively, to install into a new environment, run:

conda create -n envname dram

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/dram:<tag>

(see dram/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.

Notes¶

Databases are required. Please run 'DRAM-setup.py prepare_databases' with the respective options.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/dram/README.html)