recipe ensembl-vep

Ensembl Variant Effect Predictor

Homepage:

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

License:

Apache-2.0

Recipe:

/ensembl-vep/meta.yaml

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:

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, 

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

• perl >=5.32.1,<6.0a0 *_perl5

• perl-bio-db-hts >=2.11

• perl-bioperl >=1.7.2

• perl-dbd-mysql

• perl-dbi

• perl-io-compress

• perl-json

• perl-perlio-gzip

• perl-sereal

• perl-set-intervaltree

• perl-text-csv

• unzip

Required By:

• gnali

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install ensembl-vep

and update with:

conda update ensembl-vep

or 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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