From 90114bf2b1b83437183a5659fb2bedc1d7b2e4ce Mon Sep 17 00:00:00 2001
From: NishaSharma14 <sharmanis14@gmail.com>
Date: Mon, 6 Nov 2023 14:56:05 +0100
Subject: [PATCH] fix; update docker installation

---
 Dockerfile                            |  6 ++++--
 app/scripts/nmr-cli/Dockerfile        |  2 --
 app/scripts/nmr-respredict/Dockerfile |  2 --
 docker-compose.yml                    | 12 +++++-------
 4 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index be2d9f6..2cf88a1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,6 @@
 FROM continuumio/miniconda3 AS nmrkit-ms
 
 ENV PYTHON_VERSION=3.10
-ENV RDKIT_VERSION=2023.03.1
 ENV OPENBABEL_VERSION=v3.1
 
 ARG RELEASE_VERSION
@@ -15,10 +14,13 @@ RUN apt-get update && \
     apt-get install -y curl && \
     conda update -n base -c defaults conda
 
+RUN apt-get update && apt-get -y install docker.io
+
 RUN conda install -c conda-forge python>=PYTHON_VERSION
-RUN conda install -c conda-forge rdkit>=RDKIT_VERSION
 RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
 
+RUN pip3 install rdkit
+
 RUN python3 -m pip install -U pip
 
 ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
diff --git a/app/scripts/nmr-cli/Dockerfile b/app/scripts/nmr-cli/Dockerfile
index 194176f..7aaf2e9 100644
--- a/app/scripts/nmr-cli/Dockerfile
+++ b/app/scripts/nmr-cli/Dockerfile
@@ -12,8 +12,6 @@ COPY package.json ./
 COPY package-lock.json ./
 RUN npm install
 
-RUN apk add docker
-
 COPY . ./
 
 #install the nmr-cli as a global package 
diff --git a/app/scripts/nmr-respredict/Dockerfile b/app/scripts/nmr-respredict/Dockerfile
index f7eabae..58d6ead 100644
--- a/app/scripts/nmr-respredict/Dockerfile
+++ b/app/scripts/nmr-respredict/Dockerfile
@@ -1,7 +1,6 @@
 FROM continuumio/miniconda3 AS nmr-respredict-ms
 
 ENV PYTHON_VERSION=3.10
-ENV RDKIT_VERSION=2023.09.1
 
 # Install runtime dependencies
 RUN apt-get update && \
@@ -11,7 +10,6 @@ RUN apt-get update && \
     conda update -n base -c defaults conda
 
 RUN conda install -c conda-forge python>=PYTHON_VERSION
-# RUN conda install -c conda-forge rdkit>=RDKIT_VERSION
 RUN python3 -m pip install -U pip
 
 RUN pip3 install rdkit
diff --git a/docker-compose.yml b/docker-compose.yml
index 97d8bff..00c8020 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -2,12 +2,14 @@ version: "3.8"
 
 services:
   web:
-    build:
-      context: ./
-      dockerfile: Dockerfile
+    # build:
+    #   context: ./
+    #   dockerfile: Dockerfile
+    image: nfdi4chem/nmrkit:dev-latest
     container_name: nmrkit-api
     volumes:
       - ./app:/code/app
+      - "/var/run/docker.sock:/var/run/docker.sock"
     ports:
       - "80:80"
     healthcheck:
@@ -29,15 +31,11 @@ services:
     entrypoint: /bin/sh
     stdin_open: true
     tty: true
-    volumes:
-      - "/var/run/docker.sock:/var/run/docker.sock"
   nmr-respredict:
     build: ./app/scripts/nmr-respredict
     entrypoint: /bin/sh
     stdin_open: true
     tty: true
-    volumes:
-      - "/var/run/docker.sock:/var/run/docker.sock"
   prometheus:
     image: prom/prometheus
     container_name: nmrkit_prometheus