recipe pathracer

PathRacer is a tool for alignment of profile HMM against assembly graph.

Homepage:

http://cab.spbu.ru/software/pathracer/

License:

GPL / GPLv2

Recipe:

/pathracer/meta.yaml

Links:

biotools: pathracer, doi: 10.1007/978-3-030-18174-1_6

PathRacer is a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies.

package pathracer

versions:

3.16.0.dev-0,  3.15.0.dev-0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc-ng:

>=9.4.0

depends libstdcxx-ng:

>=9.4.0

depends libzlib:

>=1.2.11,<1.3.0a0

depends openmp:

depends sysroot_linux-64:

2.17.*

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 pathracer

and update with::

   mamba update pathracer

To create a new environment, run:

mamba create --name myenvname pathracer

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/pathracer:<tag>

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

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