docker image working

.github/workflows/ci.yaml

@@ -21,7 +21,7 @@ jobs:
       - name: Install dependencies
         run: |
           poetry install --no-dev
-          sh install_local_depency.sh
+          sh install_local_dependency.sh
       # Before running the test you have to download the tags!
       - name: Run tests
         run: |

Dockerfile

@@ -2,15 +2,12 @@ FROM python:3.9
 
 WORKDIR /pipeline
 
-RUN pip install poetry 
-RUN pip install nltk
-RUN pip install toml
-
-COPY ./ /pipeline/
-
+RUN pip install poetry
 RUN poetry config virtualenvs.create false
-RUN poetry install --without dev
-RUN poetry shell
 
-COPY . /pipeline
+COPY ./ /pipeline
+
+RUN poetry install --no-dev
+RUN sh install_local_dependency.sh
 
+CMD ["sh", "docker_start.sh"]

docker_start.sh

@@ -0,0 +1,2 @@
+python get_data/get_fpbase_data.py allele_components/tags_fpbase.toml
+uvicorn api:app --host 0.0.0.0 --port 80

readme.md

@@ -50,12 +50,10 @@ poetry run python -m ipykernel install --user
 
 To build from the dockerfile available in the repo:
 ```
-$ docker build -t genestorian .
-$ docker run --name  genestorian_c -d genestorian:latest sleep inifinity 
-$ docker exec -it genestorian_c /bin/sh
+docker build -t genestorian_data_refinement .
+docker run -d --name genestorian_data_refinement_container -p 8000:80 genestorian_data_refinement
 
 ```
-To stop the docker: `$ docker stop genestorian_c`
 
 ## Getting the data