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Dockerfile.cellbase_load
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Dockerfile.cellbase_load
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FROM opencb/cellbase
MAINTAINER Milan Simonovic <[email protected]>
ENV REFRESHED_AT 2017-01-16
ENV ENSEMBL_REL 85
ENV BIOPERL_REL 1-6-1
ENV BIOPERL_VER 1.6.1
## ENSEMBL
#TODO have a look at https://github.com/gawbul/docker-ensembl/blob/master/Dockerfile
# need perl for ensembl api:
# see docs at http://www.ensembl.org/info/docs/api/api_installation.html
RUN apt-get update && apt-get install -y build-essential libmysqlclient-dev unzip
# ubuntu xenial comes with perl 5.22 and ensembl api doesn't yet work (UNIVERSAL import deprecated...)
RUN curl -L http://install.perlbrew.pl | bash && \
source ~/perl5/perlbrew/etc/bashrc &&\
perlbrew install --notest perl-5.18.4 && perlbrew use perl-5.18.4
# cpanm --self-upgrade && \ ?
RUN curl -L http://cpanmin.us | perl - App::cpanminus && \
cpanm install DBI && \
cpanm install DBD::mysql && \
cpanm install JSON
RUN mkdir /opt/ensembl
## ENSEMBL-API
WORKDIR /opt/ensembl
RUN wget https://github.com/bioperl/bioperl-live/archive/bioperl-release-$BIOPERL_REL.tar.gz && \
tar zxf bioperl-release-$BIOPERL_REL.tar.gz && \
mv bioperl-live-bioperl-release-$BIOPERL_REL bioperl-$BIOPERL_VER
# FTP only contains the latest version, and API VERSION MUST MATCH RELEASE VERSION!
## After downloading BioPerl we need to download the API tar ball from FTP.
## This tar ball contains all the required APIs.
## RUN wget ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz && tar zxf ensembl-api.tar.gz
RUN git clone https://github.com/Ensembl/ensembl-git-tools.git && \
export PATH=$PWD/ensembl-git-tools/bin:$PATH && \
git ensembl --clone api && \
git ensembl --checkout --branch release/$ENSEMBL_REL api
ENV PERL5LIB /opt/ensembl/ensembl/modules:/opt/ensembl/ensembl-variation/modules:/opt/ensembl/ensembl-compara/modules:/opt/ensembl/ensembl-funcgen/modules:/opt/ensembl/ensembl-io/modules:/opt/ensembl/ensembl-tools/modules:/opt/ensembl/bioperl-$BIOPERL_VER/
COPY build-cellbase.sh /opt/cellbase/build/
WORKDIR /opt/cellbase/build
RUN chmod u+x build-cellbase.sh
# tmp fix for https://github.com/opencb/cellbase/issues/309
RUN ADD gene_extra_info.pl bin/ensembl-scripts/
CMD ["build-cellbase.sh"]