recipe comparative-annotation-toolkit

A straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen

Homepage

https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit

License

APACHE / Apache 2.0

Recipe

/comparative-annotation-toolkit/meta.yaml

Links

doi: 10.1101/231118

package comparative-annotation-toolkit

(downloads) docker_comparative-annotation-toolkit

Versions

0.1-2, 0.1-1, 0.1-0

Depends augustus

>=3.3

Depends bamtools

Depends bx-python

>=0.7.1

Depends configobj

>=5.0

Depends ete3

Depends frozendict

Depends luigi

>=2.5

Depends numpy

>=1.10

Depends pandas

>=0.18

Depends pyfasta

>=0.5.2

Depends pysam

>=0.10

Depends python

2.7.*

Depends samtools

>=1.3

Depends scipy

>=0.18.1

Depends seaborn

>=0.7

Depends sqlalchemy

>=1.0

Depends toil

>=3.5

Depends ucsc-axtchain

Depends ucsc-bamtopsl

Depends ucsc-bedsort

Depends ucsc-bedtobigbed

Depends ucsc-blat

Depends ucsc-chainmergesort

Depends ucsc-clustergenes

Depends ucsc-fatotwobit

Depends ucsc-genepredtobed

Depends ucsc-genepredtofakepsl

Depends ucsc-genepredtogtf

Depends ucsc-gff3togenepred

Depends ucsc-gtftogenepred

Depends ucsc-pslcdnafilter

Depends ucsc-pslcheck

Depends ucsc-pslmap

Depends ucsc-pslmappostchain

Depends ucsc-pslpostarget

Depends ucsc-pslrecalcmatch

Depends ucsc-psltobigpsl

Depends ucsc-transmappsltogenepred

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install comparative-annotation-toolkit

and update with:

conda update comparative-annotation-toolkit

or use the docker container:

docker pull quay.io/biocontainers/comparative-annotation-toolkit:<tag>

(see comparative-annotation-toolkit/tags for valid values for <tag>)