recipe biopet-validateannotation

ValidateAnnotationvalidates whether an annotation file is correct.

Homepage:

https://github.com/biopet/validateannotation

License:

MIT

Recipe:

/biopet-validateannotation/meta.yaml

ValidateAnnotationvalidates whether an annotation file is correct. It checks whether all the annotated contigs are present on the reference. It can check gtf or refflat files. It can also check both, in which case it will also check for dissimilarities between the refflat and GTF files.

For documentation and manuals visit our github.io page: https://biopet.github.io/validateannotation

package biopet-validateannotation

versions:

0.1-1,  0.1-0

depends openjdk:

>=8,<9

depends python:

requirements:

additional platforms:

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 biopet-validateannotation

and update with::

   mamba update biopet-validateannotation

To create a new environment, run:

mamba create --name myenvname biopet-validateannotation

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/biopet-validateannotation:<tag>

(see `biopet-validateannotation/tags`_ for valid values for ``<tag>``)

Notes

biopet-validateannotation is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-validateannotation'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-validateannotation -Xms512m -Xmx1g'.

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