updated docker file for environmental variables

PolusAI · Apr 23, 2024 · 704d345 · 704d345
1 parent 30d5f2b
commit 704d345
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Showing 4 changed files with 28 additions and 7 deletions.
diff --git a/utils/omero-download-tool/Dockerfile b/utils/omero-download-tool/Dockerfile
@@ -1,11 +1,19 @@
-FROM polusai/bfio:2.3.6
+FROM continuumio/miniconda3
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
 ENV POLUS_LOG="INFO"
 
+ARG OMERO_USERNAME
+ARG OMERO_PASSWORD
+ENV OMERO_USERNAME=$OMERO_USERNAME
+ENV OMERO_PASSWORD=$OMERO_PASSWORD
+
+
+ARG conda_env=myenv
+
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
@@ -15,6 +23,11 @@ COPY VERSION ${EXEC_DIR}
 COPY README.md ${EXEC_DIR}
 COPY src ${EXEC_DIR}/src
 
+RUN conda env create -f environment.yml
+
+ENV PATH /opt/conda/envs/myenv/bin:$PATH
+RUN /bin/bash -c "source activate myenv"
+
 RUN pip3 install ${EXEC_DIR} --no-cache-dir
 
 ENTRYPOINT ["python3", "-m", "polus.images.utils.omero_download"]

diff --git a/utils/omero-download-tool/README.md b/utils/omero-download-tool/README.md
@@ -41,4 +41,5 @@ This plugin takes 2 input arguments and
 
 
 ## Sample docker command:
-```docker run -v /home/ec2-user/data/:/home/ec2-user/data/ polusai/omero-download-tool:0.1.0-dev0 --dataType="plate" --id=108 --outDir=/home/ec2-user/data/output```
+```bash
+docker run -e OMERO_USERNAME=$OMERO_USERNAME -e OMERO_PASSWORD=$OMERO_PASSWORD -v /home/ec2-user/data/:/home/ec2-user/data/ polusai/omero-download-tool:0.1.0-dev0 --dataType="plate" --id=108 --outDir=/home/ec2-user/data/output```
diff --git a/utils/omero-download-tool/environment.yml b/utils/omero-download-tool/environment.yml
@@ -3,13 +3,11 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - python=3.9
-  - numpy=1.21.0
+  - python==3.9.18
+  - numpy==1.21.0
+  - bfio=*
   - ome:omero-py
-  - requests=*
-  - tqdm=*
   - pydantic=*
-  - cryptography=*
   - pip
   - pip:
     - preadator==0.4.0-dev2
diff --git a/utils/omero-download-tool/pyproject.toml b/utils/omero-download-tool/pyproject.toml
@@ -10,6 +10,10 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = "3.9.18"
+bfio = {version = "^2.3.6", extras = ["all"]}
+numpy = "1.21.0"
+typer = "^0.7.0"
+pydantic = "^2.5.3"
 
 [[tool.poetry.source]]
 name = "test"
@@ -30,3 +34,8 @@ ruff = "^0.0.270"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]