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update Java 8 installation resource and Hail version #408

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merged 3 commits into from
Sep 3, 2023
Merged

update Java 8 installation resource and Hail version #408

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7661354
update hail version to 0.1.120 & java 8 source
KoalaQin Aug 25, 2023
52e39d3
solve conflicted PyYaml versions
KoalaQin Aug 25, 2023
5a53258
change Hail to 0.2.121
KoalaQin Aug 29, 2023
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9 changes: 5 additions & 4 deletions gnomad_qc/v4/annotations/Dockerfile_vrs084_v4
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ RUN apt-get -y update && apt-get install -y --no-install-recommends \
software-properties-common \
unzip \
wget \
apt-transport-https \
zlib1g-dev \
libpq-dev \
python-dev\
Expand All @@ -34,9 +35,8 @@ RUN apt-get -y update && apt-get install -y --no-install-recommends \
rm -rf /var/lib/apt/lists/*

# Install Java 8 for hail
RUN wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - \
&& add-apt-repository -y https://adoptopenjdk.jfrog.io/adoptopenjdk/deb/ \
&& apt-get update && apt-get install -y adoptopenjdk-8-hotspot
RUN mkdir -p /etc/apt/keyrings
RUN wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc && echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list && apt-get update && apt install -y --no-install-recommends temurin-8-jdk

RUN mkdir tools
WORKDIR /tools
Expand Down Expand Up @@ -79,9 +79,10 @@ RUN python3 -m pip install --upgrade pip
# Including packages needed for VRS annotation functionality
# Also include version for ga4gh.vrs-python to be most recent and supporting their new variant schema
# Please update the constant VRS_VERSION in vrs_annotation_batch.py accordingly when GA4GH_VRS_VERSION is changed
ENV HAIL_VERSION="0.2.113"
ENV HAIL_VERSION="0.2.121"
ENV GA4GH_VRS_VERSION="0.8.4"
RUN python3 --version
RUN python3 -m pip install --ignore-installed PyYAML
RUN python3 -m pip install \
wheel \
pypandoc \
Expand Down