From 70de725445921a03aad958627703007a090c99fe Mon Sep 17 00:00:00 2001 From: Rasool Saghaleyni Date: Fri, 13 Sep 2024 00:43:23 +0200 Subject: [PATCH] Add session gems workflow --- session_gems/Dockerfile | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/session_gems/Dockerfile b/session_gems/Dockerfile index 2e66320..ed09f19 100644 --- a/session_gems/Dockerfile +++ b/session_gems/Dockerfile @@ -11,9 +11,16 @@ COPY start-script.sh /usr/local/bin/start-script.sh # Switch to root user to perform installations USER root -RUN apt-get update && apt-get install curl unzip -y --no-install-recommends && \ +RUN apt-get update && apt-get install curl git -y --no-install-recommends && \ apt-get clean && rm -rf /var/lib/apt/lists/* +# Clone the data folder from GitHub +RUN git clone --depth=1 --filter=blob:none --sparse https://github.com/NBISweden/workshop_omics_integration.git /tmp/repo && \ + cd /tmp/repo && \ + git sparse-checkout set session_gems/lab/data && \ + mv session_gems/lab/data /home/jovyan/lab/data && \ + rm -rf /tmp/repo + # Install pip requirements as root RUN pip install --no-cache-dir -r /tmp/requirements.txt