From 501d1eb884871f42a2c112b947337e1ea82c1b2d Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Mon, 24 Nov 2025 16:46:17 -0500 Subject: [PATCH 1/4] attempt 1 nf dev image --- nextflow-dev/Dockerfile | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 nextflow-dev/Dockerfile diff --git a/nextflow-dev/Dockerfile b/nextflow-dev/Dockerfile new file mode 100644 index 0000000..fd195a9 --- /dev/null +++ b/nextflow-dev/Dockerfile @@ -0,0 +1,12 @@ +FROM python:3.12 + +# from https://stackoverflow.com/questions/54131066/ +RUN set -ex && \ + apt-get update && apt-get install curl build-essential zip wget -y + +RUN set -ex && curl -s https://get.sdkman.io | bash +RUN /bin/bash -c "source /root/.sdkman/bin/sdkman-init.sh; sdk version; sdk install java 17.0.10-tem ; sdk install gradle 9.2.1" +ENV PATH="/root/.sdkman/candidates/java/current/bin/:$PATH" +RUN java -version && \ + pip install nf-core && \ + curl -s https://get.nextflow.io | bash From 135e217e6f3c8853bd142334d7da72df186ba655 Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Mon, 24 Nov 2025 16:55:51 -0500 Subject: [PATCH 2/4] add manifest --- build_manifest.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/build_manifest.csv b/build_manifest.csv index 0c9188f..bf466f7 100755 --- a/build_manifest.csv +++ b/build_manifest.csv @@ -43,3 +43,4 @@ micom,0.37.0 sylph,0.6.1a dvc,0.0.1 fmhfunprofiler,20250930 +nextflow-dev,0.0.0 From 24797fe855d33a3848e3b18eb0c0daa3fd7cb172 Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Mon, 1 Dec 2025 16:18:32 -0500 Subject: [PATCH 3/4] swap base image --- build_manifest.csv | 2 +- nextflow-dev/Dockerfile | 16 +++++++--------- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/build_manifest.csv b/build_manifest.csv index bf466f7..85d4472 100755 --- a/build_manifest.csv +++ b/build_manifest.csv @@ -43,4 +43,4 @@ micom,0.37.0 sylph,0.6.1a dvc,0.0.1 fmhfunprofiler,20250930 -nextflow-dev,0.0.0 +nextflow-dev,0.0.1 diff --git a/nextflow-dev/Dockerfile b/nextflow-dev/Dockerfile index fd195a9..b23917f 100644 --- a/nextflow-dev/Dockerfile +++ b/nextflow-dev/Dockerfile @@ -1,12 +1,10 @@ -FROM python:3.12 +FROM eclipse-temurin:25-alpine -# from https://stackoverflow.com/questions/54131066/ -RUN set -ex && \ - apt-get update && apt-get install curl build-essential zip wget -y - -RUN set -ex && curl -s https://get.sdkman.io | bash -RUN /bin/bash -c "source /root/.sdkman/bin/sdkman-init.sh; sdk version; sdk install java 17.0.10-tem ; sdk install gradle 9.2.1" -ENV PATH="/root/.sdkman/candidates/java/current/bin/:$PATH" +RUN apk add --no-cache curl gcc zip wget python3 py3-pip gradle bash git tar unzip python3-dev musl-dev linux-headers +#RUN /bin/bash -c "source /root/.sdkman/bin/sdkman-init.sh; sdk version; sdk install java 17.0.10-tem ; sdk install gradle 9.2.1 ; which gradle" +#ENV PATH="/root/.sdkman/candidates/java/current/bin/:$PATH" +ENV PIP_BREAK_SYSTEM_PACKAGES=1 RUN java -version && \ pip install nf-core && \ - curl -s https://get.nextflow.io | bash + curl -s https://get.nextflow.io | bash +RUN mv nextflow /usr/local/bin/ From b8b90d584c191657e255f60348d1651c8717849e Mon Sep 17 00:00:00 2001 From: Nick Waters Date: Mon, 1 Dec 2025 17:04:12 -0500 Subject: [PATCH 4/4] change base from alpine --- build_manifest.csv | 2 +- nextflow-dev/Dockerfile | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/build_manifest.csv b/build_manifest.csv index 85d4472..b1096a2 100755 --- a/build_manifest.csv +++ b/build_manifest.csv @@ -43,4 +43,4 @@ micom,0.37.0 sylph,0.6.1a dvc,0.0.1 fmhfunprofiler,20250930 -nextflow-dev,0.0.1 +nextflow-dev,0.0.2 diff --git a/nextflow-dev/Dockerfile b/nextflow-dev/Dockerfile index b23917f..858ed9c 100644 --- a/nextflow-dev/Dockerfile +++ b/nextflow-dev/Dockerfile @@ -1,6 +1,6 @@ -FROM eclipse-temurin:25-alpine +FROM eclipse-temurin:25 -RUN apk add --no-cache curl gcc zip wget python3 py3-pip gradle bash git tar unzip python3-dev musl-dev linux-headers +RUN apt-get update && apt-get install curl build-essential zip wget python3 pip gradle bash git unzip python3-dev -y #RUN /bin/bash -c "source /root/.sdkman/bin/sdkman-init.sh; sdk version; sdk install java 17.0.10-tem ; sdk install gradle 9.2.1 ; which gradle" #ENV PATH="/root/.sdkman/candidates/java/current/bin/:$PATH" ENV PIP_BREAK_SYSTEM_PACKAGES=1