Package Recipe 'brass' — Bioconda documentation

recipe brass

BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.

Homepage:: cancerit/BRASS
License:: AGPL-3-0
Recipe:: /brass/meta.yaml

package brass#

Versions:

5.1.6-7, 5.1.6-2

Depends:

on bedtools
on blat
on cansam
on exonerate
on libgcc
on perl-bio-db-hts
on perl-bio-featureio
on perl-bioperl-core ==1.6.924
on perl-capture-tiny
on perl-file-sharedir
on perl-file-sharedir-install
on perl-graph-readwrite
on perl-grass
on perl-math-combinatorics
on perl-number-format
on perl-pcap
on perl-statistics-basic
on perl-text-diff
on velvet

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 brass

to add into an existing workspace instead, run:

pixi add brass

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 brass

Alternatively, to install into a new environment, run:

conda create -n envname brass

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/brass:<tag>

(see brass/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/brass/README.html)