recipe thapbi-pict

THAPBI Phytophthora ITS1 Classifier Tool (PICT).

Homepage:

https://github.com/peterjc/thapbi-pict

Documentation:

https://thapbi-pict.readthedocs.io/en/latest/

License:

MIT / MIT

Recipe:

/thapbi-pict/meta.yaml

THAPBI Phytophthora ITS1 Classifier Tool (PICT) an ITS1-based diagnostic/profiling tool from the UK BBSRC funded Tree Health and Plant Biosecurity Initiative (THAPBI) Phyto-Threats project, focused on identifying Phytophthora species present in Illumina sequenced environmental samples.

package thapbi-pict

(downloads) docker_thapbi-pict

versions:
1.0.13-01.0.12-01.0.11-01.0.10-01.0.9-01.0.8-01.0.7-01.0.6-01.0.5-0

1.0.13-01.0.12-01.0.11-01.0.10-01.0.9-01.0.8-01.0.7-01.0.6-01.0.5-01.0.4-01.0.3-01.0.2-01.0.1-01.0.0-00.14.1-00.14.0-00.13.6-00.13.5-00.13.4-00.13.3-00.13.2-00.13.1-00.13.0-00.12.9-00.12.8-00.12.7-00.12.6-00.12.5-00.12.4-00.12.3-00.12.2-00.12.1-00.12.0-00.11.6-00.11.5-00.11.4-00.11.3-00.11.2-00.11.1-00.11.0-00.10.6-00.10.5-00.10.4-00.10.3-00.10.2-00.10.1-00.9.9-00.9.8-00.9.7-00.9.6-00.9.5-00.9.4-00.9.3-00.9.2-00.9.1-00.9.0-00.8.4-00.8.2-00.8.1-00.8.0-00.7.11-00.7.10-00.7.9-00.7.8-00.7.7-00.7.6-00.7.5-00.7.4-00.7.3-00.7.2-00.7.1-00.7.0-00.6.15-00.6.14-00.6.13-00.6.11-00.6.10-00.6.9-00.6.8-00.6.7-00.6.6-00.6.5-00.6.4-00.6.3-00.6.1-10.6.1-00.6.0-00.5.8-00.5.7-00.5.6-00.5.5-00.5.4-00.5.1-00.5.0-00.4.19-00.4.18-00.4.17-00.4.15-00.4.13-00.4.12-00.4.11-00.4.9-00.4.8-00.4.7-00.4.6-00.4.4-00.4.2-00.4.1-00.4.0-00.3.11-00.3.10-00.3.9-00.3.8-00.3.7-00.3.4-00.3.1-00.2.5-00.2.3-00.2.2-00.2.1-00.1.12-00.1.10-00.1.6-0

depends biom-format:

>=2.1.14

depends biopython:

>=1.82

depends blast:

depends cutadapt:

>=4.0

depends flash:

>=1.2.11

depends graphviz:

depends matplotlib-base:

>=3.7

depends networkx:

>=2.4,!=2.8.3,!=2.8.4

depends pydot:

depends python:

>=3.8

depends rapidfuzz:

>=2.4.0

depends sqlalchemy:

>=2.0

depends vsearch:

depends xlsxwriter:

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 thapbi-pict

and update with::

   mamba update thapbi-pict

To create a new environment, run:

mamba create --name myenvname thapbi-pict

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/thapbi-pict:<tag>

(see `thapbi-pict/tags`_ for valid values for ``<tag>``)

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