recipe tritimap

Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae.

Homepage:

https://github.com/fei0810/Triti-Map

Documentation:

https://github.com/fei0810/Triti-Map/wiki

License:

MIT

Recipe:

/tritimap/meta.yaml

Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae, which contains a suite of user-friendly computational packages and web-interface integrating multi-omics data from Triticeae species including genomic, epigenomic, evolutionary and homologous information.

Triti-Map could efficiently explore trait-related genes or functional elements not present in the reference genome and reduce the time and labor required for gene mapping in large genome species.

package tritimap

versions:

0.9.7-0,  0.9.6-0,  0.9.5-0,  0.9.4-0,  0.9.3-0,  0.9.2-0,  0.9.1-0,  0.9.0-0

depends abyss:

2.0.2.*

depends bedops:

2.4.39.*

depends bioawk:

depends biopython:

depends blast:

>=2.5.0

depends bwa:

0.7.17.*

depends bwa-mem2:

2.2.1.*

depends click:

>=7

depends fastp:

>=0.20.1

depends gatk4:

>=4.2.0

depends hmmer:

3.3.2.*

depends minimap2:

>=2.17

depends python:

3.9.2.*

depends r-base:

4.0.2.*

depends r-jsonlite:

1.7.2.*

depends r-qtlseqr:

0.7.5.2.*

depends samtools:

1.12.*

depends seqkit:

>=0.15.0

depends snakemake:

>=6.0.3

depends spades:

3.15.0.*

depends star:

2.7.6a.*

depends xmltramp2:

3.1.1.*

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 tritimap

and update with::

   mamba update tritimap

To create a new environment, run:

mamba create --name myenvname tritimap

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/tritimap:<tag>

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

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