From 181882e47880ab757522183508a3a64092bbea93 Mon Sep 17 00:00:00 2001
From: Manuel Lera Ramirez <manulera14@gmail.com>
Date: Tue, 31 Oct 2023 17:34:05 +0000
Subject: [PATCH] docker image working

---
 .github/workflows/ci.yaml                         |  2 +-
 Dockerfile                                        | 15 ++++++---------
 docker_start.sh                                   |  2 ++
 dummy.py                                          |  1 -
 ...ocal_depency.sh => install_local_dependency.sh |  0
 readme.md                                         |  6 ++----
 6 files changed, 11 insertions(+), 15 deletions(-)
 create mode 100644 docker_start.sh
 delete mode 100644 dummy.py
 rename install_local_depency.sh => install_local_dependency.sh (100%)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 03dbdc4..8a37682 100644
--- a/.github/workflows/ci.yaml
+++ b/.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: |
diff --git a/Dockerfile b/Dockerfile
index 13f643b..49e72f8 100644
--- a/Dockerfile
+++ b/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"]
diff --git a/docker_start.sh b/docker_start.sh
new file mode 100644
index 0000000..0a19999
--- /dev/null
+++ b/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
diff --git a/dummy.py b/dummy.py
deleted file mode 100644
index b9f4f2a..0000000
--- a/dummy.py
+++ /dev/null
@@ -1 +0,0 @@
-from genestorian_module.build_nltk_tags import build_nltk_tag
diff --git a/install_local_depency.sh b/install_local_dependency.sh
similarity index 100%
rename from install_local_depency.sh
rename to install_local_dependency.sh
diff --git a/readme.md b/readme.md
index 2f7b1a3..5bf0c82 100644
--- a/readme.md
+++ b/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