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Dockerfile
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FROM nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04
MAINTAINER Diana Sousa (dfsousa@lasige.di.fc.ul.pt)
WORKDIR /
# --------------------------------------------------------------
# GENERAL SET UP
# --------------------------------------------------------------
RUN apt-get update -y && apt-get install wget -y && apt-get install curl -y && apt-get install nano -y
# --------------------------------------------------------------
# COPY REPOSITORY DIRECTORIES
# --------------------------------------------------------------
COPY bin/DiShIn/ bin/DiShIn/
COPY src/ src/
COPY corpora/ corpora/
COPY data/ data/
COPY models/ models/
COPY results/ results/
COPY temp/ temp/
# --------------------------------------------------------------
# PYTHON LIBRARIES AND CONFIGURATION
# --------------------------------------------------------------
RUN apt-get update && apt-get install -y python3 python3-pip python3-dev && apt-get autoclean -y
RUN pip3 install --upgrade setuptools
RUN pip3 install tensorflow-gpu
RUN pip3 install gensim==3.1.0
RUN pip3 install Keras==2.1.5
RUN pip3 install numpy==1.16.4
RUN pip3 install rdflib
RUN pip3 install sklearn==0.0
RUN pip3 install matplotlib
RUN apt-get update && apt-get install -y git && apt-get autoclean -y
RUN git clone https://github.com/dpavot/obonet
RUN cd obonet && python3 setup.py install
RUN pip3 install fuzzywuzzy==0.15.1
RUN pip3 install spacy==2.0.10
RUN pip3 install scipy==1.1.0
RUN pip3 install python-Levenshtein==0.12.0
RUN pip3 install pandas
RUN python3 -m spacy download en_core_web_sm
RUN pip3 install h5py==2.0.10
# --------------------------------------------------------------
# GENIASS (REQUIRES RUBY AND MAKE)
# --------------------------------------------------------------
WORKDIR /bin
RUN mkdir geniass
WORKDIR /geniass
RUN git clone https://github.com/dpavot/geniass.git
#RUN wget -q http://www.nactem.ac.uk/y-matsu/geniass/geniass-1.00.tar.gz && \
# tar -xvzf geniass-1.00.tar.gz && \
# rm geniass-1.00.tar.gz
WORKDIR geniass
RUN apt-get update -y && apt-get install -y build-essential g++ make && make
# --------------------------------------------------------------
# SST LIGHT 0.4
# --------------------------------------------------------------
WORKDIR /bin
RUN apt-get update && apt-get install -y zip && apt-get autoclean -y
RUN wget -q https://sourceforge.net/projects/supersensetag/files/sst-light/sst-light-0.4/sst-light-0.4.tar.gz && \
tar -xvzf sst-light-0.4.tar.gz && \
rm sst-light-0.4.tar.gz
WORKDIR sst-light-0.4
#RUN apt-get update -y && make (error to solve)
# --------------------------------------------------------------
# DiShIn
# --------------------------------------------------------------
WORKDIR /bin/DiShIn/
RUN wget -q ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl
RUN wget -q http://labs.rd.ciencias.ulisboa.pt/dishin/chebi.db
RUN wget -q www.geneontology.org/ontology/go.owl
RUN wget -q http://labs.rd.ciencias.ulisboa.pt/dishin/go.db
RUN wget -q http://purl.obolibrary.org/obo/hp.owl
RUN wget -q http://labs.rd.ciencias.ulisboa.pt/dishin/hp.db
RUN wget -q https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.owl
RUN wget -q http://labs.rd.ciencias.ulisboa.pt/dishin/do.db
#RUN git clone git@github.com:lasigeBioTM/DiShIn.git
WORKDIR /data
RUN wget -q ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo
RUN wget -q http://purl.obolibrary.org/obo/hp.obo
RUN wget -q http://purl.obolibrary.org/obo/go.obo
RUN wget -q https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo
RUN wget -q http://evexdb.org/pmresources/vec-space-models/PubMed-w2v.bin
RUN export CUDA_VISIBLE_DEVICES=1,3,0
WORKDIR /