From 24f0db884ffbc97dd6fa21ba8d4694a2a777ba51 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 16 Mar 2026 13:56:24 -0400 Subject: [PATCH 1/3] copy rclone --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 02e57b85..e10d99f8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -85,10 +85,11 @@ RUN Rscript -e "options(pkgType='binary'); renv::restore(repos = c(CRAN = 'https && rm -rf /tmp/downloaded_packages \ && rm -rf /tmp/Rtmp* -# copy aws, salmon, and fastp binaries from the build image +# copy aws, rclone, salmon, and fastp binaries from the build image COPY --from=build /usr/local/aws-cli/ /usr/local/aws-cli/ RUN ln -s /usr/local/aws-cli/v2/current/bin/aws /usr/local/bin/aws RUN ln -s /usr/local/aws-cli/v2/current/bin/aws_completer /usr/local/bin/aws_completer +COPY --from=build /usr/bin/rclone /usr/local/bin/rclone COPY --from=build /usr/local/salmon/ /usr/local/ COPY --from=build /usr/local/bin/fastp /usr/local/bin/fastp From d5ea84a46aea71fa27b50670e28670446a8f69b8 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 16 Mar 2026 15:24:58 -0400 Subject: [PATCH 2/3] install rclone later, and add more comments --- Dockerfile | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index e10d99f8..3f48ea49 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -# Build salmon from source in a separate image +# Build awsli, fastp, and salmon from source in a separate image # matching base image from https://github.com/rocker-org/rocker-versioned2/blob/master/dockerfiles/r-ver_4.5.2.Dockerfile FROM docker.io/library/ubuntu:noble AS build @@ -30,9 +30,6 @@ RUN curl -o awscliv2.zip "https://awscli.amazonaws.com/awscli-exe-linux-$(arch). RUN unzip awscliv2.zip RUN ./aws/install -# Get rclone -RUN curl -L https://rclone.org/install.sh | bash - # Build salmon ARG SALMON_VERSION=1.10.3 RUN curl -LO https://github.com/COMBINE-lab/salmon/archive/refs/tags/v${SALMON_VERSION}.tar.gz @@ -69,6 +66,9 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \ fastqc \ && apt-get clean +# Get rclone +RUN curl -L https://rclone.org/install.sh | bash + # Python packages COPY requirements.txt requirements.txt RUN pip install -r requirements.txt --break-system-packages @@ -85,11 +85,10 @@ RUN Rscript -e "options(pkgType='binary'); renv::restore(repos = c(CRAN = 'https && rm -rf /tmp/downloaded_packages \ && rm -rf /tmp/Rtmp* -# copy aws, rclone, salmon, and fastp binaries from the build image +# copy aws, salmon, and fastp binaries from the build image COPY --from=build /usr/local/aws-cli/ /usr/local/aws-cli/ RUN ln -s /usr/local/aws-cli/v2/current/bin/aws /usr/local/bin/aws RUN ln -s /usr/local/aws-cli/v2/current/bin/aws_completer /usr/local/bin/aws_completer -COPY --from=build /usr/bin/rclone /usr/local/bin/rclone COPY --from=build /usr/local/salmon/ /usr/local/ COPY --from=build /usr/local/bin/fastp /usr/local/bin/fastp From 3eda5e22133dec1f7daac0a84f9e4831c94996f9 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 16 Mar 2026 15:25:20 -0400 Subject: [PATCH 3/3] speeling --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3f48ea49..3567dd8d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -# Build awsli, fastp, and salmon from source in a separate image +# Build awscli, fastp, and salmon from source in a separate image # matching base image from https://github.com/rocker-org/rocker-versioned2/blob/master/dockerfiles/r-ver_4.5.2.Dockerfile FROM docker.io/library/ubuntu:noble AS build