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Adding initial versions of gtf-smash Docker image #139

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merged 2 commits into from
Nov 27, 2024
Merged

Adding initial versions of gtf-smash Docker image #139

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408fa06
Adding initial versions of gtf-smash Docker image
tefirman Nov 27, 2024
441ef6f
Fixing linting errors for gtf-smash
tefirman Nov 27, 2024
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26 changes: 26 additions & 0 deletions gtf-smash/Dockerfile_latest
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Original file line number Diff line number Diff line change
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# 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 --no-install-recommends wget=1.21.3-1+b2 && \
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

Check failure on line 22 in gtf-smash/Dockerfile_latest

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GitHub Actions / hadolint 

DL3047 info: Avoid use of wget without progress bar. Use `wget --progress=dot:giga <url>`. Or consider using `-q` or `-nv` (shorthands for `--quiet` or `--no-verbose`).

# Installing packages via pip
RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0

Check failure on line 25 in gtf-smash/Dockerfile_latest

View workflow job for this annotation

GitHub Actions / hadolint 

DL3059 info: Multiple consecutive `RUN` instructions. Consider consolidation.

26 changes: 26 additions & 0 deletions gtf-smash/Dockerfile_v8
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Original file line number Diff line number Diff line change
@@ -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 --no-install-recommends wget=1.21.3-1+b2 && \
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

Check failure on line 22 in gtf-smash/Dockerfile_v8

View workflow job for this annotation

GitHub Actions / hadolint 

DL3047 info: Avoid use of wget without progress bar. Use `wget --progress=dot:giga <url>`. Or consider using `-q` or `-nv` (shorthands for `--quiet` or `--no-verbose`).

# Installing packages via pip
RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0

Check failure on line 25 in gtf-smash/Dockerfile_v8

View workflow job for this annotation

GitHub Actions / hadolint 

DL3059 info: Multiple consecutive `RUN` instructions. Consider consolidation.