Package Recipe 'comparative-annotation-toolkit'

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:: ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
License:: APACHE / Apache 2.0
Recipe:: /comparative-annotation-toolkit/meta.yaml
Links:: doi: 10.1101/231118

package comparative-annotation-toolkit#

Versions:

0.1-2, 0.1-1, 0.1-0

Depends:

on augustus >=3.3
on bamtools
on bx-python >=0.7.1
on configobj >=5.0
on ete3
on frozendict
on luigi >=2.5
on numpy >=1.10
on pandas >=0.18
on pyfasta >=0.5.2
on pysam >=0.10
on python 2.7.*
on samtools >=1.3
on scipy >=0.18.1
on seaborn >=0.7
on sqlalchemy >=1.0
on toil >=3.5
on ucsc-axtchain
on ucsc-bamtopsl
on ucsc-bedsort
on ucsc-bedtobigbed
on ucsc-blat
on ucsc-chainmergesort
on ucsc-clustergenes
on ucsc-fatotwobit
on ucsc-genepredtobed
on ucsc-genepredtofakepsl
on ucsc-genepredtogtf
on ucsc-gff3togenepred
on ucsc-gtftogenepred
on ucsc-pslcdnafilter
on ucsc-pslcheck
on ucsc-pslmap
on ucsc-pslmappostchain
on ucsc-pslpostarget
on ucsc-pslrecalcmatch
on ucsc-psltobigpsl
on ucsc-transmappsltogenepred

Additional platforms:

Installation#

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi#

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install comparative-annotation-toolkit

to add into an existing workspace instead, run:

pixi add comparative-annotation-toolkit

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda#

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install comparative-annotation-toolkit

Alternatively, to install into a new environment, run:

conda create -n envname comparative-annotation-toolkit

with envname being the name of the desired environment.

Container#

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment#

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page#

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/comparative-annotation-toolkit/README.html)