diff --git a/Dockerfile b/Dockerfile index 54760e9..1d257ba 100644 --- a/Dockerfile +++ b/Dockerfile @@ -28,6 +28,7 @@ RUN apt-get update \ git \ libpq-dev \ make \ + apt-utils \ python-pip \ python2.7 \ python2.7-dev \ @@ -38,27 +39,33 @@ RUN apt-get update \ && apt-get autoremove \ && apt-get clean +RUN pip install --upgrade pip RUN pip install -U "pycorenlp==0.3.0" RUN pip install -U "scipy==0.17.0" RUN pip install -U "sklearn==0.0" RUN pip install -U "requests==2.4.3" RUN pip install -U "scikit-learn==0.18.2" RUN pip install -U "matplotlib==2.0.2" +RUN pip install -U "networkx==2.2" +# RUN pip install -U "pysqlite" # this is only for webapp +RUN pip install -U "uuid" RUN wget http://nlp.stanford.edu/software/stanford-corenlp-full-2017-06-09.zip \ && unzip stanford-corenlp-full-2017-06-09.zip \ - && wget https://www.dropbox.com/s/ec3a4ey7s0k6qgy/FINAL-ner-model.AImed%2BMedTag%2BBioInfer.ser.gz?dl=0 \ + && wget https://compgen.bio.ub.edu/datasets/PPaxe_files/FINAL-ner-model.AImed%2BMedTag%2BBioInfer.ser.gz \ -O /stanford-corenlp-full-2017-06-09/FINAL-ner-model.AImed+MedTag+BioInfer.ser.gz \ && wget http://nlp.stanford.edu/software/stanford-english-corenlp-2017-06-09-models.jar \ -O /stanford-corenlp-full-2017-06-09/stanford-english-corenlp-2017-06-09-models.jar -RUN git --no-pager clone https://github.com/CompGenLabUB/ppaxe.git +RUN echo "# Installing ppaxe lib..." \ + && git --no-pager clone https://github.com/scastlara/ppaxe.git +# # repo clone at https://github.com/CompGenLabUB/ppaxe.git RUN sed -i 's%\.\./%/stanford-corenlp-full-2017-06-09/%' \ /ppaxe/ppaxe/data/server.properties WORKDIR /ppaxe -RUN wget https://www.dropbox.com/s/t6qcl19g536c0zu/RF_scikit.pkl?dl=0 \ +RUN wget https://compgen.bio.ub.edu/datasets/PPaxe_files/RF_scikit.pkl \ -O ./ppaxe/data/RF_scikit.pkl \ && pip install ./