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:

4.2.1-0,  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, 

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.*

• blast

• fastani

• fasttree

• graphviz

• iqtree

• kmc 3.0.1.*

• mafft

• mash 2.3.*

• mcl

• openjdk 8.*

• python >=3.7

• r-ape

• r-base >=3.5.0

• r-ggplot2

• tabix

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install pantools

and update with:

conda update pantools

or 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". NB: Both `BUSCO` and `bcftools` are dependencies of PanTools but they are not included in this recipe due to conflicts on MacOS.

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