conda 23.10.0 + conda-forge pip

broadinstitute · Dec 11, 2023 · da06b4a · da06b4a
1 parent 5934691
commit da06b4a
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Showing 4 changed files with 7 additions and 5 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-ARG BASE_DOCKER=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc6
+ARG BASE_DOCKER=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc6-sl
 
 # stage 1 for constructing the GATK zip
 FROM ${BASE_DOCKER} AS gradleBuild

diff --git a/scripts/docker/gatkbase/Dockerfile b/scripts/docker/gatkbase/Dockerfile
@@ -62,8 +62,8 @@ ENV JAVA_LIBRARY_PATH /usr/lib/jni
 
 # Install miniconda
 ENV DOWNLOAD_DIR /downloads
-ENV CONDA_URL https://repo.anaconda.com/miniconda/Miniconda3-py310_23.1.0-1-Linux-x86_64.sh
-ENV CONDA_SHA256 "32d73e1bc33fda089d7cd9ef4c1be542616bd8e437d1f77afeeaf7afdb019787"
+ENV CONDA_URL https://repo.anaconda.com/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh
+ENV CONDA_SHA256 "c7a34df472feb69805b64df6e8db58363c5ccab41cd3b40b07e3e6dfb924359a"
 ENV CONDA_PATH /opt/miniconda
 ENV PATH $CONDA_PATH/bin:$PATH
 RUN mkdir $DOWNLOAD_DIR && \
@@ -72,4 +72,6 @@ RUN mkdir $DOWNLOAD_DIR && \
     bash $DOWNLOAD_DIR/miniconda.sh -p $CONDA_PATH -b && \
     rm $DOWNLOAD_DIR/miniconda.sh && \
     conda clean -afy && \
+    conda config --set auto_update_conda false && \
+    conda config --set solver libmamba && \
     rm -rf /root/.cache/pip
diff --git a/scripts/docker/gatkbase/build_docker_base.sh b/scripts/docker/gatkbase/build_docker_base.sh
@@ -7,7 +7,7 @@ set -e
 REPO=broadinstitute
 PROJECT=gatk
 VERSION=2.3.0
-FULL_PATH=${REPO}/${PROJECT}:gatkbase-${VERSION}
+FULL_PATH=us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area:3.2.0rc6-sl
 
 #################################################
 # Parsing arguments

diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template
@@ -20,7 +20,7 @@ dependencies:
 
 # core python dependencies
 - conda-forge::python=3.6.10        # do not update
-- pip=20.0.2                        # specifying channel may cause a warning to be emitted by conda
+- conda-forge::pip=21.3.1
 - conda-forge::mkl=2019.5           # MKL typically provides dramatic performance increases for theano, tensorflow, and other key dependencies
 - conda-forge::mkl-service=2.3.0
 - conda-forge::joblib=1.1.1         # must pin joblib - versions after 1.1.1 no longer support python 3.6