From fa96ec4718ee1dcd3734442e7230064d5b1137cf Mon Sep 17 00:00:00 2001
From: imedina <igmecas@gmail.com>
Date: Fri, 27 Sep 2024 14:57:51 +0100
Subject: [PATCH] app: minor improvements

---
 .../cloud/docker/opencga-nextflow/Dockerfile  | 29 -------------------
 .../cloud/docker/opencga-workflow/Dockerfile  |  2 +-
 2 files changed, 1 insertion(+), 30 deletions(-)
 delete mode 100644 opencga-app/app/cloud/docker/opencga-nextflow/Dockerfile

diff --git a/opencga-app/app/cloud/docker/opencga-nextflow/Dockerfile b/opencga-app/app/cloud/docker/opencga-nextflow/Dockerfile
deleted file mode 100644
index f79fbce126..0000000000
--- a/opencga-app/app/cloud/docker/opencga-nextflow/Dockerfile
+++ /dev/null
@@ -1,29 +0,0 @@
-## Based on Ubuntu 22.04 (jammy)
-FROM eclipse-temurin:11.0.24_8-jre-jammy
-
-ARG BUILD_PATH="."
-
-RUN apt-get update && apt-get -y upgrade && apt-get install -y lsb-release sshpass ca-certificates curl gnupg jq unzip vim htop && \
-    ## Install Docker repository
-    install -m 0755 -d /etc/apt/keyrings && \
-    curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \
-    chmod a+r /etc/apt/keyrings/docker.gpg && \
-    echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu "$(. /etc/os-release && echo "jammy")" stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \
-    apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io && \
-    ## Install yq
-    wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 && \
-    chmod +x /usr/local/bin/yq && \
-    ## Install Nextflow \
-    curl -s https://get.nextflow.io | bash && \
-    chmod +xr nextflow && \
-    mv nextflow /usr/local/bin/ && \
-    ## Clean downloaded packages to make images smaller
-    rm -rf /var/lib/apt/lists/* && \
-    adduser --disabled-password --uid 1001 opencga && \
-    # Add docker group to opencga user
-    usermod -a -G docker opencga
-
-## Run Docker images as opencga user
-USER opencga
-
-WORKDIR /home/opencga
diff --git a/opencga-app/app/cloud/docker/opencga-workflow/Dockerfile b/opencga-app/app/cloud/docker/opencga-workflow/Dockerfile
index 70a536079f..8a61e16333 100644
--- a/opencga-app/app/cloud/docker/opencga-workflow/Dockerfile
+++ b/opencga-app/app/cloud/docker/opencga-workflow/Dockerfile
@@ -37,7 +37,7 @@ COPY --chown=opencga:opencga ${BUILD_PATH} ${OPENCGA_HOME}
 
 ## 2. Based on base
 FROM base
-RUN apt-get update && apt-get -y upgrade && apt-get install -y python3 python3-pip bcftools && \
+RUN apt-get update && apt-get -y upgrade && apt-get install -y python3 python3-pip r-base samtools bcftools && \
     pip3 install ${OPENCGA_HOME}/clients/python && \
     ## Clean downloaded packages to make images smaller
     rm -rf /var/lib/apt/lists/*