From bdab1ebba7bee20af21c04e6344214e298e1670d Mon Sep 17 00:00:00 2001
From: "Thouis (Ray) Jones" <thouis@broadinstitute.org>
Date: Tue, 16 Apr 2024 17:33:38 -0400
Subject: [PATCH] Add "--enable-gcs" to samtools and bcftools tool builds

This change enables network access to Google Cloud Storage buckets for samtools and bcftools.  The upstream image (terra-jupyter-python) already has this flag enabled for htslib (which these tool use, though in install, they use their own htslib by default).
---
 terra-jupyter-gatk/Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile
index b63bbb4a..f02539e6 100644
--- a/terra-jupyter-gatk/Dockerfile
+++ b/terra-jupyter-gatk/Dockerfile
@@ -55,6 +55,7 @@ RUN mkdir -p /tmp/samtools && \
     bzip2 -d samtools.tar.bz2 && \
     tar xvf samtools.tar && \
     cd samtools-1.18 && \
+    ./configure --enable-gcs && \
     make && \
     make install && \
     cd $HOME && \
@@ -67,6 +68,7 @@ RUN mkdir -p /tmp/bcftools && \
     bzip2 -d bcftools.tar.bz2 && \
     tar xvf bcftools.tar && \
     cd bcftools-1.18 && \
+    ./configure --enable-gcs && \
     make && \
     make install && \
     cd $HOME && \