From 796000c16f29071dfa805223e781d319238767ba Mon Sep 17 00:00:00 2001 From: mattjmeier Date: Fri, 19 Jan 2024 16:47:58 -0500 Subject: [PATCH] Update dockerfile --- Dockerfile | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index fa1ec6f0..ce9496f3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,6 +7,7 @@ FROM condaforge/mambaforge:23.3.1-1 as base # Required to avoid interactive prompts ARG DEBIAN_FRONTEND=noninteractive +ARG PLATFORM=temposeq # Set up a user for running; -m creates home directory, -s sets default shell RUN useradd -ms /bin/bash R-ODAF @@ -32,13 +33,10 @@ WORKDIR "/home/R-ODAF/R-ODAF_Health_Canada" COPY . . RUN chown -R R-ODAF:R-ODAF /home/R-ODAF USER R-ODAF -RUN /bin/bash -c "tree data && tree config && \ - mv data data.bak && mv config config.bak" -# Why??? -# RUN mv data data.bak && mv config config.bak +RUN rm -r inputs RUN git clone https://github.com/EHSRB-BSRSE-Bioinformatics/test-data \ -&& mv test-data/temposeq/* ./ \ +&& mv test-data/${PLATFORM}/* ./ \ && wget https://github.com/EHSRB-BSRSE-Bioinformatics/unify_temposeq_manifests/raw/main/output_manifests/Human_S1500_1.2_standardized.csv # Build environments with Snakemake