recipe 10x_bamtofastq

Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.

Homepage:

https://github.com/10XGenomics/bamtofastq

Documentation:

https://github.com/10XGenomics/bamtofastq/blob/v1.4.1/README.md

License:

MIT / MIT

Recipe:

/10x_bamtofastq/meta.yaml

Links:

usegalaxy-eu: 10x_bamtofastq

package 10x_bamtofastq

(downloads) docker_10x_bamtofastq

Versions:

1.4.1-4,  1.4.1-3,  1.4.1-2,  1.4.1-1,  1.4.1-0

Depends:

  • on libgcc >=13

  • on libstdcxx >=13

Additional platforms:
linux-aarch64,  osx-arm64

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 10x_bamtofastq

to add into an existing workspace instead, run:

pixi add 10x_bamtofastq

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 10x_bamtofastq

Alternatively, to install into a new environment, run:

conda create -n envname 10x_bamtofastq

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/10x_bamtofastq:<tag>

(see 10x_bamtofastq/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.

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