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Add rclone, redux #953

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Merged
sjspielman merged 3 commits into from
Mar 16, 2026
Merged

Add rclone, redux #953

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24f0db8
copy rclone
sjspielman Mar 16, 2026
d5ea84a
install rclone later, and add more comments
sjspielman Mar 16, 2026
3eda5e2
speeling
sjspielman Mar 16, 2026
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8 changes: 4 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Build 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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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