From 7661354fed9b8ae363aaf99182a04b7479af9cb2 Mon Sep 17 00:00:00 2001 From: Qin He <44242118+KoalaQin@users.noreply.github.com> Date: Fri, 25 Aug 2023 08:52:14 -0400 Subject: [PATCH 1/3] update hail version to 0.1.120 & java 8 source --- gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 b/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 index a632dffd0..c46bb0349 100644 --- a/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 +++ b/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 @@ -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\ @@ -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 @@ -79,7 +79,7 @@ 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="0.2.120" ENV GA4GH_VRS_VERSION="0.8.4" RUN python3 --version RUN python3 -m pip install \ From 52e39d3d4cee53595b9741ea1545409a3cc70596 Mon Sep 17 00:00:00 2001 From: Qin He <44242118+KoalaQin@users.noreply.github.com> Date: Fri, 25 Aug 2023 09:47:18 -0400 Subject: [PATCH 2/3] solve conflicted PyYaml versions --- gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 | 1 + 1 file changed, 1 insertion(+) diff --git a/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 b/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 index c46bb0349..38b42a9f3 100644 --- a/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 +++ b/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 @@ -82,6 +82,7 @@ RUN python3 -m pip install --upgrade pip ENV HAIL_VERSION="0.2.120" 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 \ From 5a53258cdbb9fef184c443197416efe0e9416606 Mon Sep 17 00:00:00 2001 From: Qin He <44242118+KoalaQin@users.noreply.github.com> Date: Tue, 29 Aug 2023 18:03:52 -0400 Subject: [PATCH 3/3] change Hail to 0.2.121 --- gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 b/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 index 38b42a9f3..ca0ea999a 100644 --- a/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 +++ b/gnomad_qc/v4/annotations/Dockerfile_vrs084_v4 @@ -79,7 +79,7 @@ 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="0.2.120" +ENV HAIL_VERSION="0.2.121" ENV GA4GH_VRS_VERSION="0.8.4" RUN python3 --version RUN python3 -m pip install --ignore-installed PyYAML