Merge pull request #445 from neurodata/tathey1-ailey

Tathey1 ailey

.gitignore

@@ -93,3 +93,5 @@ experiments/sriram/sample/
 # experiments/register_axons
 experiments/map_neurons/.ipynb_checkpoints/
 experiments/map_neurons/data/mapping-files/
+
+experiments/BrainLine/data/models/

Dockerfile

@@ -1,15 +1,54 @@
 FROM python:3.8-slim-buster
+ENV AWS_KEY=
+ENV AWS_SEC_KEY=
 
 WORKDIR /brainlit_dir
 
 RUN apt-get update && apt-get install -y gcc libgl1-mesa-glx libxrender1
-RUN apt install -y wget bzip2
+RUN apt install -y wget bzip2 vim
 
+# install ilastik
 RUN wget https://files.ilastik.org/ilastik-1.4.0-Linux.tar.bz2
 RUN tar xjf ilastik-1.4.0-Linux.tar.bz2
 
+# install brainlit
 COPY . .
 RUN pip install -e .
 
-RUN mkdir /root/.cloudvolume/
-RUN mkdir /root/.cloudvolume/secrets/
+
+RUN chmod +x ./.aws.sh
+RUN ./.aws.sh
+
+CMD python experiments/BrainLine/scripts/soma_detect_image.py
+
+# Old version
+# FROM python:3.8-slim
+# #RUN pip install --no-cache-dir matplotlib pandas numpy
+
+# WORKDIR /usr/src/app
+
+# #RUN apt-get update \
+# #    && apt-get install -y --no-install-recommends git 
+# #    && apt-get purge -y --auto-remove \
+# RUN apt-get update
+# RUN apt-get install -y --no-install-recommends \
+#     make automake gcc g++ subversion python3-dev \
+#     && rm -rf /var/lib/apt/lists/*
+
+
+# # RUN apk add --no-cache --update \
+# #     python3 python3-dev gcc \
+# #     gfortran musl-dev
+
+# # RUN apk update && apk upgrade && \
+# #     apk add --no-cache bash git openssh
+
+# # RUN git clone https://github.com/neurodata/brainlit.git
+
+# RUN pip install --upgrade pip setuptools && \
+#     pip install --no-cache-dir brainlit
+
+
+# # create credentials file for aws
+# # RUN chmod +x .aws.sh && \ 
+# #     source .aws.sh