Merge pull request #27 from MaxUlysse/VEPfix

Fixing VEP container

Author: Szilveszter Juhos

containers/vep/Dockerfile

@@ -6,6 +6,7 @@ maintainer="maxime.garcia@scilifelab.se"
 
 # Install libraries
 RUN apt-get update && apt-get install -y --no-install-recommends \
+apache2 \
 build-essential \
 ca-certificates \
 cpanminus \
@@ -14,22 +15,45 @@ git \
 libmysqlclient-dev \
 libpng12-dev \
 libssl-dev \
+manpages \
 mysql-client \
+openssl \
 perl \
 perl-base \
 unzip \
+vim \
+wget \
 && rm -rf /var/lib/apt/lists/* \
-&& cpanm DBI DBD::mysql Set::IntervalTree PerlIO::gzip
+&& cpanm DBI DBD::mysql
 
-# Setup ENV variables
-ENV PATH="$PATH:/ensembl-vep" \
-VEP_VERSION="release/90.1"
+# Set up ENV variables
+ENV CFLAGS="-fPIC" \
+DEPS="/home/vep/src" \
+HOME="/home/vep" \
+HTSLIB_DIR="/home/vep/src/htslib" \
+KENT_SRC="/home/vep/src/kent-335_base/src" \
+MACHTYPE="x86_64" \
+PATH="/home/vep/src/ensembl-vep:$PATH" \
+PERL5LIB="$PERL5LIB:/home/vep/src/bioperl-live-release-1-6-924:/home/vep/src/ensembl/modules/:/home/vep/src/ensembl-vep/modules/:/home/vep/src/ensembl-variation/modules/:/home/vep/src/ensembl-funcgen/modules/:/home/vep/src/ensembl-io/modules/"
 
-# Install VEP
-RUN git clone https://github.com/Ensembl/ensembl-vep.git ensembl-vep \
---branch $VEP_VERSION \
-&& cd ensembl-vep \
-&& perl INSTALL.pl
+# Preparing install
+RUN mkdir -p $DEPS \
+&& cd $DEPS \
+&& git clone https://github.com/Ensembl/ensembl-funcgen ensembl-funcgen \
+&& git clone https://github.com/Ensembl/ensembl-io ensembl-io \
+&& git clone https://github.com/Ensembl/ensembl-variation ensembl-variation \
+&& git clone https://github.com/Ensembl/ensembl-vep ensembl-vep \
+&& git clone https://github.com/Ensembl/ensembl ensembl \
+&& $DEPS/ensembl-vep/travisci/get_dependencies.sh \
+&& $DEPS/ensembl-vep/travisci/build_c.sh \
+&& cd $HTSLIB_DIR \
+&& make install \
+&& cpanm --installdeps --with-recommends --notest --cpanfile $DEPS/ensembl/cpanfile . \
+&& cpanm --installdeps --with-recommends --notest --cpanfile $DEPS/ensembl-vep/cpanfile .
+
+# Installing VEP
+RUN chmod u+x $DEPS/ensembl-vep/*.pl
+RUN $DEPS/ensembl-vep/INSTALL.pl -a a -l
 
 # Create UPPMAX directories
 RUN mkdir /pica /proj /sw