recipe ensembl-vep

Ensembl Variant Effect Predictor

Homepage:

https://www.ensembl.org/info/docs/tools/vep/index.html

Documentation:

https://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html

Developer docs:

https://github.com/Ensembl/ensembl-vep

License:

APACHE / Apache-2.0

Recipe:

/ensembl-vep/meta.yaml

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:

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, 

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 htslib:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-bio-db-hts:

>=2.11

depends perl-bioperl:

>=1.7.2

depends perl-dbd-mysql:

depends perl-dbi:

depends perl-io-compress:

depends perl-json:

depends perl-perlio-gzip:

depends perl-sereal:

depends perl-set-intervaltree:

depends perl-text-csv:

depends unzip:

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 ensembl-vep

and update with::

   mamba update ensembl-vep

To create a new environment, run:

mamba create --name myenvname ensembl-vep

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/ensembl-vep:<tag>

(see `ensembl-vep/tags`_ for valid values for ``<tag>``)

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

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