- recipe ensembl-vep
Ensembl Variant Effect Predictor
- Homepage:
- Documentation:
https://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
- Developer docs:
- License:
APACHE / Apache-2.0
- Recipe:
- Links:
biotools: vep
The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
- package ensembl-vep¶
- Versions:
115.2-1,115.2-0,115.1-0,115-0,114.2-1,114.2-0,114.1-0,114.0-0,113.4-0,115.2-1,115.2-0,115.1-0,115-0,114.2-1,114.2-0,114.1-0,114.0-0,113.4-0,113.3-2,113.3-1,113.3-0,113.2-0,113.0-0,112.0-0,111.0-0,110.1-0,110.0-0,109.3-1,109.3-0,108.2-0,108.1-0,108.0-0,107.0-0,106.1-0,106.0-0,105.0-1,105.0-0,104.3-1,104.3-0,104.2-1,104.2-0,104.1-1,104.1-0,104.0-0,103.1-2,103.1-1,103.1-0,102.0-0,101.0-1,101.0-0,100.4-0,100.3-0,100.2-0,100.1-1,100.1-0,100.0-0,99.2-0,99.1-0,99.0-0,98.3-0,98.2-0,98.1-0,98.0-1,98.0-0,97.4-0,97.3-0,97.2-0,97.1-0,97.0-0,96.3-0,96.0-0,95.3-0,95.2-0,95.1-0,95.0-1,95.0-0,94.5-0,94.4-0,94.0-0,93.4-0,93.2-0,92.4-0,92.3-0,92.0-1,91.3-1,91.3-0,91.2-0,91.1-0,91.0-0,90.10-0,90.9-1,90.7-1,90.7-0,90.6-0,90.5-0,90.3-0,90.1-1,90.1-0,89.7-0,89.4-0,89.1-2,89.1-1,88.10-1,88.10-0,88.9-2,88.9-1,88.9-0,88.8-0,88-0- Depends:
on htslib
on perl
>=5.32.1,<6.0a0 *_perl5on perl-bio-bigfile
on perl-bio-db-hts
>=2.11on perl-bio-procedural
on perl-bioperl
>=1.7.3on perl-dbd-mysql
on perl-dbd-sqlite
on perl-dbi
on perl-io-compress
on perl-json
on perl-list-moreutils
on perl-perlio-gzip
on perl-sereal
on perl-set-intervaltree
on perl-text-csv
on unzip
- 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 ensembl-vep
to add into an existing workspace instead, run:
pixi add ensembl-vep
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 ensembl-vep
Alternatively, to install into a new environment, run:
conda create -n envname ensembl-vep
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/ensembl-vep:<tag>
(see ensembl-vep/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.
Notes¶
This package installs only the variant effect predictor (VEP) library code. To install data libraries, you can use the 'vep_install' command installed along with it. For example, to install the VEP library for human GRCh38 to a directory
vep_install -a cf -s homo_sapiens -y GRCh38 -c /output/path/to/GRCh38/vep --CONVERT
- (note that vep_install is renamed from INSTALL.pl
to avoid having generic script names in the PATH)
The --CONVERT flag is not required but improves lookup speeds during runs. See the VEP documentation for more details
http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/ensembl-vep/README.html)
