recipe scramble

Soft Clipped Read Alignment Mapper

Homepage:

https://github.com/GeneDx/scramble

License:

CC

Recipe:

/scramble/meta.yaml

Links:

doi: 10.1038/s41436-020-0749-x

SCRAMble identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls

package scramble

(downloads) docker_scramble

Versions:

1.0.2-1,  1.0.2-0,  1.0.1-2,  1.0.1-1,  1.0.1-0

Depends:

  • on bioconductor-rsamtools >=2.4.0

  • on htslib >=1.17,<1.24.0a0

  • on libgcc-ng >=12

  • on r-base >=4.0.3

  • on r-optparse >=1.6.6

  • on r-rblast >=0.99.1

  • on r-stringr >=1.4.0

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 scramble

to add into an existing workspace instead, run:

pixi add scramble

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 scramble

Alternatively, to install into a new environment, run:

conda create -n envname scramble

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/scramble:<tag>

(see scramble/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.

Notes

SCRAMble runs as a two-step process. First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. Second, SCRAMble.R analyzes the cluster file for likely MEIs. Custom wrapper script scramble.sh is provided to help setting location of SCRAMble.R script, and values for --install-dir and --mei-refs params.

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