Package Recipe 'shannon_cpp'

recipe shannon_cpp

shannon_cpp is command line tool for denovo rna assembly

Homepage:: https://github.com/bx3/shannon_cpp.git
License:: GPL v3.0
Recipe:: /shannon_cpp/meta.yaml

package shannon_cpp¶

Versions:

0.5.0-0, 0.4.0-0

Depends:

on boost-cpp >=1.70.0,<1.70.1.0a0
on coreutils
on glpk >=4.65,<4.66.0a0
on kmer-jellyfish 2.*
on libgcc-ng >=7.3.0
on libstdcxx-ng >=7.3.0
on metis >=5.1.0,<5.2.0a0
on perl >=5.26.2,<5.26.3.0a0
on python >=2.7,<2.8.0a0
on rcorrector 1.*
on sparsehash
on wget
on zlib >=1.2.11,<1.3.0a0

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 shannon_cpp

to add into an existing workspace instead, run:

pixi add shannon_cpp

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 shannon_cpp

Alternatively, to install into a new environment, run:

conda create -n envname shannon_cpp

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/shannon_cpp:<tag>

(see shannon_cpp/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:

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