eilon-s/centos6_vep:latest
$ singularity pull shub://eilon-s/centos6_vep:latest
Singularity Recipe
Bootstrap: docker
From: willmclaren/ensembl-vep
# sudo singularity build ensembl-vep Singularity
%help
This is a singularity file for VEP docker.
run example: singularity run --bind $PWD:$PWD ensembl-vep -i ./inputfilename.vcf -o ./outputfilename --cache --assembly GRCh37 --dir_cache /opt/vep/.vep --dir_plugins /opt/vep/.plugins --offline --format vcf --vcf --symbol --plugin Downstream --plugin Wildtype --terms SO
%environment
LANGUAGE=en_US
LANG="en_US.UTF-8"
LC_ALL=C
export LANGUAGE LANG LC_ALL
%post
mkdir -p /opt/vep/.vep;
# install data for yeast BY
#perl /opt/vep/src/ensembl-vep/INSTALL.pl -a acf -s Saccharomyces_cerevisiae -y R64-1-1 -c /opt/vep/.vep;
# install data for human hg19
#perl /opt/vep/src/ensembl-vep/INSTALL.pl -a acf -s homo_sapiens -y GRCh37 -c /opt/vep/.vep
# get plugins
#rm -fr /opt/vep/.plugins;
mkdir -p /opt/vep/.plugins;
rm -f -r /VEP_plugins;
git clone https://github.com/Ensembl/VEP_plugins.git;
cp -r -f /VEP_plugins/* /opt/vep/.plugins;
rm -f -r /VEP_plugins;
# get pVACseq plugin
rm -f -r /pVAC-Seq;
git clone https://github.com/griffithlab/pVAC-Seq.git;
cp -f /pVAC-Seq/pvacseq/VEP_plugins/Wildtype.pm /opt/vep/.plugins;
rm -f -r /pVAC-Seq;
%runscript
exec /opt/vep/src/ensembl-vep/vep "$@"
%apprun vep
exec /opt/vep/src/ensembl-vep/vep "$@"
%apprun install_vep
exec perl /opt/vep/src/ensembl-vep/INSTALL.pl "$@"
Collection
- Name: eilon-s/centos6_vep
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/eilon-s-centos6_vep-latest |
collection name | eilon-s/centos6_vep |
branch | master |
tag | latest |
commit | ddb130ab869066051c2e5c3a41f89ec0191160b2 |
version (container hash) | 8af692060443e6c221ed69e92c2544ba |
build date | 2018-05-13T10:34:44.154Z |
size (MB) | 1637 |
size (bytes) | 620933151 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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