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Fixing a permissions issue in gtf-smash #140

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merged 2 commits into from
Nov 27, 2024
Merged

Fixing a permissions issue in gtf-smash #140

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9089619
Fixing permissions errors for gtf-smash
tefirman Nov 27, 2024
ba863af
Fixing permissions errors for gtf-smash
tefirman Nov 27, 2024
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6 changes: 5 additions & 1 deletion gtf-smash/Dockerfile_latest
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,11 @@
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
WORKDIR /usr/gtf-smash
RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py && \

Check failure on line 23 in gtf-smash/Dockerfile_latest

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`).
chmod +x collapse_annotation.py
WORKDIR /
ENV PATH="${PATH}:/usr/gtf-smash"

# Installing packages via pip
RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0
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6 changes: 5 additions & 1 deletion gtf-smash/Dockerfile_v8
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,11 @@
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
WORKDIR /usr/gtf-smash
RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py && \

Check failure on line 23 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`).
chmod +x collapse_annotation.py
WORKDIR /
ENV PATH="${PATH}:/usr/gtf-smash"

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