From 9089619fe5b669fd54ef6cb9ad77468858a282d1 Mon Sep 17 00:00:00 2001 From: tefirman Date: Tue, 26 Nov 2024 20:01:31 -0800 Subject: [PATCH 1/2] Fixing permissions errors for gtf-smash --- gtf-smash/Dockerfile_latest | 3 ++- gtf-smash/Dockerfile_v8 | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/gtf-smash/Dockerfile_latest b/gtf-smash/Dockerfile_latest index b08a180..01297b8 100644 --- a/gtf-smash/Dockerfile_latest +++ b/gtf-smash/Dockerfile_latest @@ -19,7 +19,8 @@ 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 +RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py && \ + chmod +x 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 index 3ab98b0..d022a32 100644 --- a/gtf-smash/Dockerfile_v8 +++ b/gtf-smash/Dockerfile_v8 @@ -19,7 +19,8 @@ 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 +RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py && \ + chmod +x collapse_annotation.py # Installing packages via pip RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0 From ba863af291f400260ce90af1b4b771475227cf6c Mon Sep 17 00:00:00 2001 From: tefirman Date: Tue, 26 Nov 2024 20:33:06 -0800 Subject: [PATCH 2/2] Fixing permissions errors for gtf-smash --- gtf-smash/Dockerfile_latest | 3 +++ gtf-smash/Dockerfile_v8 | 3 +++ 2 files changed, 6 insertions(+) diff --git a/gtf-smash/Dockerfile_latest b/gtf-smash/Dockerfile_latest index 01297b8..63c5b8a 100644 --- a/gtf-smash/Dockerfile_latest +++ b/gtf-smash/Dockerfile_latest @@ -19,8 +19,11 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* # Pulling down collapse_annotation.py script from GitHub +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="${PATH}:/usr/gtf-smash" # Installing packages via pip RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0 diff --git a/gtf-smash/Dockerfile_v8 b/gtf-smash/Dockerfile_v8 index d022a32..4fff0ac 100644 --- a/gtf-smash/Dockerfile_v8 +++ b/gtf-smash/Dockerfile_v8 @@ -19,8 +19,11 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* # Pulling down collapse_annotation.py script from GitHub +WORKDIR /usr/gtf-smash RUN wget https://raw.githubusercontent.com/broadinstitute/gtex-pipeline/refs/tags/gtex_v8/gene_model/collapse_annotation.py && \ chmod +x collapse_annotation.py +WORKDIR / +ENV PATH="${PATH}:/usr/gtf-smash" # Installing packages via pip RUN pip install --no-cache-dir pandas==2.2.3 bx-python==0.13.0