recipe rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

Homepage:

https://github.com/smangul1/rop

License:

GPL-3.0

Recipe:

/rop/meta.yaml

package rop

versions:

1.1.2-3,  1.1.2-2,  1.1.2-1,  1.1.2-0,  1.1.1-0

depends biopython:

depends blast:

depends bowtie2:

depends bwa:

depends fastx_toolkit:

depends intervaltree:

depends kmer-jellyfish:

depends libgcc-ng:

>=9.3.0

depends numpy:

depends pandas:

depends pysam:

depends python:

>=2.7,<2.8.0a0

depends python_abi:

2.7.* *_cp27mu

depends samtools:

depends scikit-learn:

depends scipy:

depends tophat:

requirements:

Installation

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 rop

and update with::

   mamba update rop

To create a new environment, run:

mamba create --name myenvname rop

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 quay.io/biocontainers/rop:<tag>

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

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