recipe mintie

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Homepage:

https://github.com/Oshlack/MINTIE

License:

MIT

Recipe:

/mintie/meta.yaml

package mintie

versions:

0.4.3-0,  0.4.2-0,  0.4.1-0,  0.3.9-0

depends bbmap:

depends bedtools:

depends bioconductor-edger:

depends bioconductor-tximport:

depends biopython:

depends bpipe:

depends fastuniq:

depends fastx_toolkit:

depends gmap:

>=2021.06.04

depends intervaltree_bio:

depends numpy:

depends pandas:

depends pybedtools:

depends pysam:

depends python:

depends r-base:

depends r-data.table:

depends r-dplyr:

depends r-jsonlite:

depends r-readr:

depends r-statmod:

depends salmon:

depends samtools:

depends soapdenovo-trans:

1.03.*

depends tbb:

2020.2.*

depends trimmomatic:

requirements:

additional platforms:

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 mintie

and update with::

   mamba update mintie

To create a new environment, run:

mamba create --name myenvname mintie

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/mintie:<tag>

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

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