recipe eastr-cpp

Detect and remove spuriously spliced alignments from RNA-seq data

Homepage:

https://github.com/ishinder/eastr-cpp

Documentation:

https://github.com/ishinder/eastr-cpp#readme

License:

MIT / MIT

Recipe:

/eastr-cpp/meta.yaml

Links:

doi: 10.1038/s41467-023-43017-4, biotools: eastr

EASTR (Emending Alignments of Spliced Transcript Reads) identifies and eliminates systematic alignment errors in multi-exon genes from RNA-seq data. This C++ implementation provides ~10x faster performance than the original Python version with identical results.

package eastr-cpp

versions:

2.0.2-0

depends bowtie2:

>=2.5.2

depends htslib:

>=1.23,<1.24.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

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 eastr-cpp

and update with::

   mamba update eastr-cpp

To create a new environment, run:

mamba create --name myenvname eastr-cpp

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/eastr-cpp:<tag>

(see `eastr-cpp/tags`_ for valid values for ``<tag>``)

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