From 046134d73d1158fc567fb57dc54c8ff2df66cf95 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Tue, 8 Oct 2024 19:04:31 -0700 Subject: [PATCH 1/2] Fix #370 20.04 (focal) base image --> sed 4.7.1 even after upgrade 24.04 (jammy) base image --> usher fails to build 22.04 as the base image builds and installs sed 4.8 --- install/Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/install/Dockerfile b/install/Dockerfile index 386b5c15..3a293d2d 100644 --- a/install/Dockerfile +++ b/install/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:20.04 +FROM ubuntu:22.04 ENV APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=DontWarn ENV DEBIAN_FRONTEND=noninteractive USER root @@ -6,6 +6,8 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \ git wget \ ca-certificates \ sudo python3 python3-pip +RUN apt-get upgrade -y sed +# faSomeRecords and faSize are needed for the UShER WDL workflow WORKDIR /HOME/kentsource RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSize @@ -16,6 +18,5 @@ WORKDIR usher ## Checkout latest release #RUN git checkout $(git describe --tags `git rev-list --tags --max-count=1`) RUN ./install/installUbuntu.sh -# faSomeRecords and faSize are needed for the UShER WDL workflow ## set the path ENV PATH="/HOME/usher/build:/HOME/kentsource:${PATH}" From bc4f0f159c4bd034a06035fe4e3d7e5c4ca891a4 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Tue, 8 Oct 2024 19:19:02 -0700 Subject: [PATCH 2/2] Remove redundant sed install --- install/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/install/Dockerfile b/install/Dockerfile index 3a293d2d..c9f6c4fe 100644 --- a/install/Dockerfile +++ b/install/Dockerfile @@ -6,7 +6,6 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \ git wget \ ca-certificates \ sudo python3 python3-pip -RUN apt-get upgrade -y sed # faSomeRecords and faSize are needed for the UShER WDL workflow WORKDIR /HOME/kentsource RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords