recipe efishent

A tool to design RNA FISH oligos/probes






package efishent

(downloads) docker_efishent



depends biopython:

depends blast:

depends bowtie:

depends entrez-direct:

depends gtfparse:

depends jellyfish:

depends luigi:

depends matplotlib-base:

depends numpy:

depends pandas:

depends pyarrow:

depends pyomo:

depends pysam:

depends python:


depends rnastructure:

depends samtools:

depends tqdm:



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 efishent

and update with::

   mamba update efishent

To create a new environment, run:

mamba create --name myenvname efishent

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 `efishent/tags`_ for valid values for ``<tag>``)

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