From 511ea086c0facf1fc4b31fe9fbbbcf5ab6dbef5b Mon Sep 17 00:00:00 2001
From: LizBaldo <baldo@broadinstitute.org>
Date: Mon, 27 Nov 2023 15:03:42 -0500
Subject: [PATCH] try to also update samtools

---
 config/conf.json                | 2 +-
 terra-jupyter-aou/CHANGELOG.md  | 3 ++-
 terra-jupyter-aou/Dockerfile    | 2 +-
 terra-jupyter-gatk/CHANGELOG.md | 6 ++++++
 terra-jupyter-gatk/Dockerfile   | 6 +++++-
 5 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/config/conf.json b/config/conf.json
index fbb80b59..75685d4e 100644
--- a/config/conf.json
+++ b/config/conf.json
@@ -124,7 +124,7 @@
             "packages" : {
                 
             },
-            "version" : "2.3.5",
+            "version" : "2.3.6",
             "automated_flags" : {
                 "include_in_ui" : true,
                 "generate_docs" : true,
diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md
index 9914d591..9b34047c 100644
--- a/terra-jupyter-aou/CHANGELOG.md
+++ b/terra-jupyter-aou/CHANGELOG.md
@@ -1,7 +1,8 @@
 ## 2.2.8 - 2023-11-14T15:56:44.507726350Z
 
-- Update `terra-jupyter-r` to `2.2.4`
+- Update `terra-jupyter-gatk` to `2.3.6`
   - Bioconductor 3.18 release
+  - Samtools 1.18
 
 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.8`
 
diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile
index bd2f3a76..25e710eb 100644
--- a/terra-jupyter-aou/Dockerfile
+++ b/terra-jupyter-aou/Dockerfile
@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.5
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.6
 
 USER root
 
diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md
index 3abfe6b0..caa47023 100644
--- a/terra-jupyter-gatk/CHANGELOG.md
+++ b/terra-jupyter-gatk/CHANGELOG.md
@@ -1,3 +1,9 @@
+## 2.3.5 - 2023-11-27
+
+- Update Samtools to `1.18`
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.6`
+
 ## 2.3.5 - 2023-11-14T15:56:44.486168932Z
 
 - Update `terra-jupyter-r` to `2.2.4`
diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile
index dd80821d..e5b9ac3f 100644
--- a/terra-jupyter-gatk/Dockerfile
+++ b/terra-jupyter-gatk/Dockerfile
@@ -16,7 +16,7 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \
   liblzo2-dev \
   zlib1g-dev \
   libz-dev \
-  samtools \
+  samtools==1.18 \
   git-lfs \
   && apt-get clean \
   && rm -rf /var/lib/apt/lists/*
@@ -79,6 +79,10 @@ COPY cnn-models.patch /etc/gatk-$GATK_VERSION/cnn-models.patch
 
 RUN patch -u /opt/conda/lib/python3.10/site-packages/vqsr_cnn/vqsr_cnn/models.py -i /etc/gatk-$GATK_VERSION/cnn-models.patch
 
+# Older version of nbconvert fail to convert notebooks to html
+RUN pip3 install "nbconvert>=7.7.3"
+
+
 ENV PIP_USER=true
 
 ENV USER jupyter