- recipe earlgrey
Earl Grey: A fully automated TE curation and annotation pipeline.
- Homepage:
- Documentation:
- License:
OSL-2.1
- Recipe:
- Links:
Earl Grey is a full-automated transposable element (TE) annotation pipeline, leveraging the most widely-used tools and combining these with a consensus elongation process (BEAT) to better define de novo consensus sequences when annotating new genome assemblies.
- package earlgrey¶
- Versions:
7.1.0-0,7.0.3-0,7.0.2-0,7.0.1-1,7.0.1-0,7.0.0-0,6.3.6-0,6.3.5-0,6.3.4-0,7.1.0-0,7.0.3-0,7.0.2-0,7.0.1-1,7.0.1-0,7.0.0-0,6.3.6-0,6.3.5-0,6.3.4-0,6.3.3-0,6.3.2-0,6.3.1-0,6.3.0-0,6.2.0-1,6.2.0-0,6.1.1-0,6.1.0-0,6.0.3-0,6.0.1-0,6.0.0-0,5.1.1-0,5.1.0-1,5.1.0-0,5.0.3-0,5.0.0-2,5.0.0-1,5.0.0-0,4.5.0-2,4.5.0-1,4.5.0-0,4.4.5-1,4.4.5-0,4.4.4-0,4.4.1-0,4.4.0-0,4.3.0-0,4.2.4-1,4.2.4-0,4.2.3-0,4.1.1-1,4.1.1-0,4.1.0-0,4.0.8-0,4.0.7-0,4.0.6-0,4.0.5-0,4.0.4-0,4.0.3-0,4.0.2-0,4.0.1-1,4.0.1-0,4.0-1,4.0-0,3.2.2-0,3.2.1-0,3.2-0,3.1-0- Depends:
on bedtools
on bioconductor-bsgenome
on bioconductor-genomeinfodb
on bioconductor-genomeinfodbdata
on bioconductor-plyranges
on cd-hit
on emboss
on genometools-genometools
on heliano
on hmmer
on libgcc
>=14on libstdcxx
>=14on ltr_retriever
on mafft
on mreps
on ncls
on ninja-nj
on pandas
on parallel
on pybedtools
on pyfaidx
on pyranges
on python
on r-ape
on r-cowplot
on r-data.table
on r-ggtext
on r-kableextra
on r-magrittr
on r-optparse
on r-plyr
on r-tidyverse
on r-viridis
on recon
on repeatmasker
4.2.2.*on repeatmodeler
>=2.0.4on repeatscout
on samtools
on trf
- 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 earlgrey
to add into an existing workspace instead, run:
pixi add earlgrey
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 earlgrey
Alternatively, to install into a new environment, run:
conda create -n envname earlgrey
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/earlgrey:<tag>
(see earlgrey/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¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/earlgrey/README.html)
