Merge pull request #140 from getwilds/gtf-fix

Fixing a permissions issue in gtf-smash
getwilds · Nov 27, 2024 · 71a76ab · 71a76ab
2 parents 73f1a85 + ba863af
commit 71a76ab
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diff --git a/gtf-smash/Dockerfile_latest b/gtf-smash/Dockerfile_latest
@@ -19,7 +19,11 @@ RUN apt-get update && \
     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 && \
+    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

diff --git a/gtf-smash/Dockerfile_v8 b/gtf-smash/Dockerfile_v8
@@ -19,7 +19,11 @@ RUN apt-get update && \
     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 && \
+    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