Package Recipe 'optilcms'

recipe optilcms

Pipeline for processing LC-MS raw data with optimized parameters.

Homepage:: https://github.com/xia-lab/OptiLCMS
License:: MIT / MIT
Recipe:: /optilcms/meta.yaml

package optilcms¶

Versions:

1.1.0-0

Depends:

on bioconductor-biobase
on bioconductor-biocparallel >=1.8.0
on bioconductor-biocstyle
on bioconductor-graph
on bioconductor-massspecwavelet
on bioconductor-msnbase
on bioconductor-mtbls2
on bioconductor-mzr >=2.22.0
on bioconductor-rbgl
on bioconductor-s4vectors
on r-base >=4.3,<4.4.0a0
on r-cairo
on r-cluster
on r-data.table
on r-entropy
on r-ggplot2
on r-ggrepel
on r-hmisc
on r-knitr >=1.1.0
on r-lattice
on r-maldiquant
on r-plyr
on r-progress
on r-rcolorbrewer
on r-rcpp >=1.0.9
on r-rjsonio
on r-rmarkdown
on r-rsm
on r-scales
on r-xml

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 optilcms

to add into an existing workspace instead, run:

pixi add optilcms

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 optilcms

Alternatively, to install into a new environment, run:

conda create -n envname optilcms

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/optilcms:<tag>

(see optilcms/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/optilcms/README.html)