Merge pull request #140 from getwilds/gtf-fix

Fixing a permissions issue in gtf-smash

Author: tefirman

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

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