<commit_before>FROM viapath/snappy_ngstools:flatdog
MAINTAINER <NAME> <<EMAIL>>
ENV HOME /home/vagrant
ENV DEBIAN_FRONTEND noninteractive
ENV PERL_MM_USE_DEFAULT=1
ENV CACHEDIR ${HOME}/work/vep

# install mysql
RUN apt-get install -y mysql-client mysql-server libmysqlclient-dev

# install required perl modules
RUN cpan -i Archive::Extract DBI DBD::mysql CGI Archive::Zip File::Copy::Recursive JSON Sereal

# download and extract VEP GRCh37
RUN cd /usr/local/pipeline && \
    wget -c https://github.com/Ensembl/ensembl-tools/archive/release/84.zip && \
    unzip 84.zip && \
    rm 84.zip

# install VEP
ENV PATH /usr/local/pipeline/ensembl-tools-release-84/scripts/variant_effect_predictor/htslib:$PATH
ENV PERL5LIB /usr/local/pipeline/ensembl-tools-release-84/scripts/variant_effect_predictor:$PERL5LIB
RUN mkdir -p /home/vagrant/work
RUN cd /usr/local/pipeline/ensembl-tools-release-84/scripts/variant_effect_predictor && \
    perl INSTALL.pl --AUTO ap \
    --PLUGINS all \
    --NO_HTSLIB
ADD  Grantham.pm ${HOME}/.vep/Plugins


CMD ["/bin/bash"]

## usage:
## perl variant_effect_predictor.pl -i my_input.vcf -fork 4 -cache -vcf --ASSEMBLY GRCh37<commit_msg>fixed grantham score plugin<commit_after>FROM viapath/snappy_ngstools:flatdog
MAINTAINER <NAME> <<EMAIL>>
#ENV HOME /home/vagrant
ENV DEBIAN_FRONTEND noninteractive
ENV PERL_MM_USE_DEFAULT=1
ENV CACHEDIR ${HOME}/work/vep

# install mysql
RUN apt-get install -y mysql-client mysql-server libmysqlclient-dev

# install required perl modules
RUN cpan -i Archive::Extract DBI DBD::mysql CGI Archive::Zip File::Copy::Recursive JSON Sereal

# download and extract VEP GRCh37
RUN cd /usr/local/pipeline && \
    wget -c https://github.com/Ensembl/ensembl-tools/archive/release/84.zip && \
    unzip 84.zip && \
    rm 84.zip

# install VEP
ENV VEPINSTALL /usr/local/pipeline/ensembl-tools-release-84/scripts/variant_effect_predictor
ENV PATH $VEPINSTALL/htslib:$PATH
ENV PERL5LIB $VEPINSTALL:$PERL5LIB
RUN cd $VEPINSTALL && \
    perl INSTALL.pl --AUTO ap \
    --PLUGINS all \
    --NO_HTSLIB

# add own plugins
ADD Grantham.pm $VEPINSTALL

CMD ["/bin/bash"]

## usage:
## perl variant_effect_predictor.pl -i my_input.vcf -fork 4 -cache -vcf --ASSEMBLY GRCh37
{'fraction_non_alphanumeric': 0.11531531531531532, 'fraction_numerical': 0.016216216216216217, 'mean_word_length': 4.12933025404157, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3355435', 'n_tokens_mistral': 854, 'n_tokens_neox': 816, 'n_words': 190}