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Fix installing less in Dockerfile
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HippocampusGirl committed Oct 9, 2023
1 parent b4a062e commit 106d65a
Showing 1 changed file with 13 additions and 8 deletions.
21 changes: 13 additions & 8 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
FROM sbtscala/scala-sbt:eclipse-temurin-jammy-19.0.1_10_1.9.0_3.2.2 as builder

COPY src/extract-all /src/extract-all
RUN cd /src/extract-all \
&& sbt assembly
RUN cd /src/extract-all && \
sbt assembly

FROM apache/hadoop:3
USER root
Expand All @@ -22,11 +22,18 @@ RUN mkdir -p -v /localdata/liftover && \
RUN mkdir -p -v /localdata/imputationserver && \
wget --progress=dot:giga -O "/localdata/imputationserver/1000genomes-phase3.zip" "https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-3.0.0.zip"

RUN yum install -y less which && \
yum clean all -y && \
sync && \
rm -rf /var/cache/yum && \
rm -rf /tmp/* && \
sync

# Install Cloudgene.
ENV CLOUDGENE_VERSION=2.6.3
RUN mkdir /opt/cloudgene \
&& cd /opt/cloudgene \
&& curl --silent install.cloudgene.io | bash -s ${CLOUDGENE_VERSION}
RUN mkdir /opt/cloudgene && \
cd /opt/cloudgene && \
curl --silent install.cloudgene.io | bash -s ${CLOUDGENE_VERSION}
ENV PATH="/opt/cloudgene:/usr/local/mambaforge/bin:${PATH}" \
CPATH="/usr/local/mambaforge/include:${CPATH}"

Expand Down Expand Up @@ -57,9 +64,7 @@ RUN wget --progress=dot:giga -O "/tmp/conda.sh" "https://github.com/conda-forge/
"plink" \
"plink2" \
"tabix>=1.11" \
"ucsc-liftover" \
"m2-less" \
"which" && \
"ucsc-liftover" && \
sync && \
mamba clean --yes --all --force-pkgs-dirs && \
sync && \
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