Package Recipe 'cellsnake'

recipe cellsnake

cellsnake, a user-friendly tool for single cell RNA sequencing analysis

Homepage:: https://github.com/sinanugur/cellsnake
License:: MIT
Recipe:: /cellsnake/meta.yaml

package cellsnake¶

Versions:

0.2.0.12-0, 0.2.0.11-2, 0.2.0.11-1, 0.2.0.11-0, 0.2.0-1, 0.2.0-0, 0.2.0.dev9-0

Depends:

on bedtools
on celltypist 1.3.0
on cmake
on docopt
on fastp
on fuzzywuzzy
on geos 3.11.1
on hdf5
on kraken2
on levenshtein
on matplotlib-base <3.7
on numba >=0.56.4
on openblas 0.3.21
on pandas <=1.5.3
on plotly
on pysam >=0.16.0.1
on python
on r-clustree 0.5.0
on r-cowplot
on r-curl
on r-dbplyr <=2.3.2
on r-expm
on r-fields
on r-ggalluvial
on r-ggpubr
on r-ggraph 2.1.0
on r-ggthemes
on r-gplots
on r-hdf5r
on r-igraph
on r-librarian
on r-matrix <=1.5_4.1
on r-minqa
on r-nmf
on r-openxlsx
on r-optparse
on r-patchwork
on r-plotly
on r-r.utils
on r-randomcolor
on r-reticulate
on r-rsvd
on r-seurat 4.3.0
on r-seuratobject 4.1.3
on r-spdep
on r-terra
on r-tidyseurat
on r-tidyverse
on r-v8
on r-viridis
on r-xml
on regex >=2021.4.4
on samtools
on scanpy 1.9.1
on scipy
on snakemake-minimal 7.22.0
on umap-learn

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 cellsnake

to add into an existing workspace instead, run:

pixi add cellsnake

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 cellsnake

Alternatively, to install into a new environment, run:

conda create -n envname cellsnake

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/cellsnake:<tag>

(see cellsnake/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/cellsnake/README.html)