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Add Dockerfile and fix requirements #171

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Add Dockerfile and fix requirements #171

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a657c4d
Fix broken requirements
leoramme Nov 22, 2021
747b03e
Add Dockerfile
leoramme Nov 22, 2021
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19 changes: 19 additions & 0 deletions Dockerfile
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FROM tensorflow/tensorflow:1.15.5-gpu-py3

RUN apt-get update -y && apt-get install -y python3-dev build-essential wget

COPY . /app

WORKDIR /app

RUN pip install -r requirements.txt

RUN ./download.sh

ENV BIOBERT_DIR=./biobert_v1.1_pubmed

ENV NER_DIR=./datasets/NER/NCBI-disease

ENV OUTPUT_DIR=./ner_outputs

RUN mkdir -p $OUTPUT_DIR
8 changes: 4 additions & 4 deletions requirements.txt
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tensorflow-gpu==1.15.2 # GPU version of TensorFlow >= 1.11.0. (should be under 2.0.0)

tensorflow-gpu==1.15.5 # GPU version of TensorFlow >= 1.11.0. (should be under 2.0.0)
numpy==1.18.0


# To evaluate RE answers :
sklearn
pandas==0.23
scikit-learn==0.24.2
pandas==1.1.5

# To evaluate BioASQ answers, your system should be able to execute java codes.
# Please refer https://github.com/BioASQ/Evaluation-Measures for details.