From 408fa063c2e6459be7146f7fdf07cd114d18069a Mon Sep 17 00:00:00 2001 From: tefirman Date: Tue, 26 Nov 2024 19:36:45 -0800 Subject: [PATCH 1/2] Adding initial versions of gtf-smash Docker image --- gtf-smash/Dockerfile_latest | 26 ++++++++++++++++++++++++++ gtf-smash/Dockerfile_v8 | 26 ++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 gtf-smash/Dockerfile_latest create mode 100644 gtf-smash/Dockerfile_v8 diff --git a/gtf-smash/Dockerfile_latest b/gtf-smash/Dockerfile_latest new file mode 100644 index 0000000..664f17f --- /dev/null +++ b/gtf-smash/Dockerfile_latest @@ -0,0 +1,26 @@ + +# Using Python base image +FROM python:3.12-slim + +# Adding labels for the GitHub Container Registry +LABEL org.opencontainers.image.title="gtf-smash" +LABEL org.opencontainers.image.description="Container image for the use of the gtf collapser necessary for RNASeQC" +LABEL org.opencontainers.image.version="latest" +LABEL org.opencontainers.image.authors="wilds@fredhutch.org" +LABEL org.opencontainers.image.url=https://hutchdatascience.org/ +LABEL org.opencontainers.image.documentation=https://getwilds.org/ +LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library +LABEL org.opencontainers.image.licenses=MIT + +# Installing wget +RUN apt-get update && \ + apt-get install -y wget && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +# Pulling down collapse_annotation.py script from GitHub +RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py + +# Installing packages via pip +RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0 + diff --git a/gtf-smash/Dockerfile_v8 b/gtf-smash/Dockerfile_v8 new file mode 100644 index 0000000..9ec6e18 --- /dev/null +++ b/gtf-smash/Dockerfile_v8 @@ -0,0 +1,26 @@ + +# Using Python base image +FROM python:3.12-slim + +# Adding labels for the GitHub Container Registry +LABEL org.opencontainers.image.title="gtf-smash" +LABEL org.opencontainers.image.description="Container image for the use of the gtf collapser necessary for RNASeQC" +LABEL org.opencontainers.image.version="v8" +LABEL org.opencontainers.image.authors="wilds@fredhutch.org" +LABEL org.opencontainers.image.url=https://hutchdatascience.org/ +LABEL org.opencontainers.image.documentation=https://getwilds.org/ +LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library +LABEL org.opencontainers.image.licenses=MIT + +# Installing wget +RUN apt-get update && \ + apt-get install -y wget && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +# Pulling down collapse_annotation.py script from GitHub +RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py + +# Installing packages via pip +RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0 + From 441ef6fd20d2fe53d0153f422ed49ff2440ff27d Mon Sep 17 00:00:00 2001 From: tefirman Date: Tue, 26 Nov 2024 19:43:52 -0800 Subject: [PATCH 2/2] Fixing linting errors for gtf-smash --- gtf-smash/Dockerfile_latest | 2 +- gtf-smash/Dockerfile_v8 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gtf-smash/Dockerfile_latest b/gtf-smash/Dockerfile_latest index 664f17f..b08a180 100644 --- a/gtf-smash/Dockerfile_latest +++ b/gtf-smash/Dockerfile_latest @@ -14,7 +14,7 @@ LABEL org.opencontainers.image.licenses=MIT # Installing wget RUN apt-get update && \ - apt-get install -y wget && \ + apt-get install -y --no-install-recommends wget=1.21.3-1+b2 && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* diff --git a/gtf-smash/Dockerfile_v8 b/gtf-smash/Dockerfile_v8 index 9ec6e18..3ab98b0 100644 --- a/gtf-smash/Dockerfile_v8 +++ b/gtf-smash/Dockerfile_v8 @@ -14,7 +14,7 @@ LABEL org.opencontainers.image.licenses=MIT # Installing wget RUN apt-get update && \ - apt-get install -y wget && \ + apt-get install -y --no-install-recommends wget=1.21.3-1+b2 && \ apt-get clean && \ rm -rf /var/lib/apt/lists/*