recipe pantools

PanTools is a pangenomic toolkit for comparative analysis of large numbers of genomes.

Homepage:

https://git.wur.nl/bioinformatics/pantools

Documentation:

https://pantools.readthedocs.io/

License:

GPL / GPL-3.0-only

Recipe:

/pantools/meta.yaml

Links:

doi: https://doi.org/10.1093/bioinformatics/btw455, doi: https://doi.org/10.1186/s12859-018-2362-4, doi: https://doi.org/10.1101/813634, doi: https://doi.org/10.1093/bioinformatics/btac506

PanTools is a pangenomic toolkit for comparative analysis of large numbers of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.

package pantools

versions:

4.3.1-0,  4.3.0-0,  4.2.3-1,  4.2.3-0,  4.2.2-0,  4.2.1-0,  4.2.0-0,  4.1.1-0,  4.1.0-0, 

4.3.1-0,  4.3.0-0,  4.2.3-1,  4.2.3-0,  4.2.2-0,  4.2.1-0,  4.2.0-0,  4.1.1-0,  4.1.0-0,  4.0.0-1,  4.0.0-0,  3.4.0-0,  3.3.3-0,  3.1.0-1,  3.1.0-0,  2.0.0-0,  1.2-1,  1.2-0,  1.0-0

depends aster:

1.3.*

depends bcftools:

>=1.12

depends blast:

depends busco:

5.*

depends fastani:

depends fasttree:

depends graphviz:

depends iqtree:

depends kmc:

>=3.1.0

depends mafft:

depends mash:

2.3.*

depends mcl:

depends openjdk:

8.*

depends pal2nal:

>=14.1

depends paml:

>=4.10.6

depends python:

>=3.7

depends r-ape:

depends r-base:

>=3.5.0

depends r-cowplot:

>=1.1.1

depends r-ggplot2:

depends tabix:

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 pantools

and update with::

   mamba update pantools

To create a new environment, run:

mamba create --name myenvname pantools

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/pantools:<tag>

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

Notes

PanTools is Java program that comes with a custom wrapper Python script. This wrapper is called "pantools" and is on $PATH by default. By default "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "pantools -Xms512m -Xmx1g".

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