recipe clinker

Clinker is a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc), that can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.






package clinker

(downloads) docker_clinker



depends bioconductor-biomart:

depends bioconductor-gviz:

depends bpipe:

depends python:


depends samtools:

depends star:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install clinker

and update with::

   mamba update clinker

To create a new environment, run:

mamba create --name myenvname clinker

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `clinker/tags`_ for valid values for ``<tag>``)


Wrapper script provided to indicate clinker is a bpipe pipeline, provide example command from wiki, and also a passthrough option.

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