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FROM tensorflow/tensorflow:2.9.1
RUN apt-get update && apt-get install -y git unzip wget curl
RUN pip3 install --upgrade pip cmake
WORKDIR scDrug
COPY requirements.txt requirements.txt
RUN pip3 install -r requirements.txt
COPY . .
## scMatch
RUN git clone https://github.com/asrhou/scMatch.git /opt/scMatch
RUN unzip /opt/scMatch/refDB/FANTOM5/10090_HID.csv.zip -d /opt/scMatch/refDB/FANTOM5/ && rm /opt/scMatch/refDB/FANTOM5/10090_HID.csv.zip
RUN unzip /opt/scMatch/refDB/FANTOM5/10090_symbol.csv.zip -d /opt/scMatch/refDB/FANTOM5/ && rm /opt/scMatch/refDB/FANTOM5/10090_symbol.csv.zip
RUN unzip /opt/scMatch/refDB/FANTOM5/9606_HID.csv.zip -d /opt/scMatch/refDB/FANTOM5/ && rm /opt/scMatch/refDB/FANTOM5/9606_HID.csv.zip
RUN unzip /opt/scMatch/refDB/FANTOM5/9606_symbol.csv.zip -d /opt/scMatch/refDB/FANTOM5/ && rm /opt/scMatch/refDB/FANTOM5/9606_symbol.csv.zip
RUN sed -i 's/\.ix/.loc/g' /opt/scMatch/scMatch.py
RUN sed -i 's/loc\[commonRows, ].fillna(0\.0)/reindex(commonRows, axis="index", fill_value=0.0)/g' /opt/scMatch/scMatch.py
# survival analysis
RUN wget -q https://figshare.com/ndownloader/files/35612942 -O data/TCGA.zip
RUN unzip data/TCGA.zip
RUN rm data/TCGA.zip
## CaDRReS-Sc
RUN git clone https://github.com/CSB5/CaDRReS-Sc.git /opt/CaDRReS-Sc
RUN wget -q --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=19d5kIP2YlChqLFZZo4aWoU2maspa9oe1' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=19d5kIP2YlChqLFZZo4aWoU2maspa9oe1" -O /opt/CaDRReS-Sc/data/GDSC/GDSC_exp.tsv && rm -rf /tmp/cookies.txt
RUN mkdir -p /opt/CaDRReS-Sc/data/CCLE
RUN wget -q --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=19lU6RnCjx57Oj0UZlpIwieHYTYdxc7MN' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=19lU6RnCjx57Oj0UZlpIwieHYTYdxc7MN" -O /opt/CaDRReS-Sc/data/CCLE/CCLE_expression.csv && rm -rf /tmp/cookies.txt
RUN mkdir -p /opt/CaDRReS-Sc/preprocessed_data/PRISM
RUN wget -q --no-check-certificate 'https://docs.google.com/uc?export=download&id=1AhjNbT88--PmG8qZSOcF_C2tYm-FoC2c' -O /opt/CaDRReS-Sc/preprocessed_data/PRISM/PRISM_drug_info.csv
RUN wget -q --no-check-certificate 'https://docs.google.com/uc?export=download&id=1_TCD-OO-l1dsnwLoLlb8eD92grE6_ZPU' -O /opt/CaDRReS-Sc/preprocessed_data/PRISM/feature_genes.txt
RUN sed -i 's/import tensorflow as tf/import tensorflow.compat.v1 as tf\ntf.disable_v2_behavior()/g' /opt/CaDRReS-Sc/cadrres_sc/model.py
RUN sed -i 's/import tensorflow\.python\.util\.deprecation as deprecation/from tensorflow.python.util import deprecation/g' /opt/CaDRReS-Sc/cadrres_sc/model.py
## CIBERSORTx
RUN curl -fsSL https://get.docker.com -o get-docker.sh
RUN sh get-docker.sh
CMD [ "/bin/bash" ]