Slim down docker images.

This removes deepvariant from the image, for the time being.  For some reason
these images have ballooned in size since the last time we built them, and
that is stopping them from being successfully uploaded to quay.

Summary of changes to reduce image sizes:

- remove deepvariant
- remove .a and .pyc files from image
- use conda clean -fay to more aggressive clean up after conda.

Dockerfile.base

@@ -1,5 +1,6 @@
 # Build bcbio base image with code and framework
 
+#FROM continuumio/miniconda
 FROM ubuntu:18.04
 LABEL maintainer="bcbio (https://github.com/bcbio/bcbio-nextgen)"
 ARG git_revision=master
@@ -17,7 +18,7 @@ RUN apt-get update && \
       https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
     python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
       --isolate --minimize-disk --nodata -u development --revision "$git_revision" && \
-    /usr/local/share/bcbio-nextgen/anaconda/bin/conda install -y nomkl && \
+#    /usr/local/share/bcbio-nextgen/anaconda/bin/conda install -y nomkl && \
     /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade -u development --revision "$git_revision" && \
 # add user run script
     wget --no-check-certificate -O createsetuser \
@@ -30,7 +31,8 @@ RUN apt-get update && \
     cd /usr/local && \ 
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /var/tmp/* && \
-    /usr/local/share/bcbio-nextgen/anaconda/bin/conda clean --yes --tarballs --packages && \
+#    /usr/local/share/bcbio-nextgen/anaconda/bin/conda clean --yes --tarballs --packages && \
+    /usr/local/share/bcbio-nextgen/anaconda/bin/conda clean -afy && \
     /usr/local/share/bcbio-nextgen/anaconda/bin/conda build purge-all && \
     rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/qt* && \
     rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/scipy-0.19.1-np113py27_nomkl_0 && \
@@ -53,6 +55,10 @@ RUN apt-get update && \
 # Ensure permissions are set for update in place by arbitrary users
     find /usr/local -perm /u+x -execdir chmod a+x {} \; && \
     find /usr/local -perm /u+w -execdir chmod a+w {} \; && \
+# remove unneeded files .a .pyc
+    find /usr/local/share/bcbio-nextgen -follow -type f -name "*.pyc" -delete && \
+    find /usr/local/share/bcbio-nextgen -follow -type f -name "*.a" -delete && \
+    find /usr/local/share/bcbio-nextgen -follow -type f -name "*.js.map" -delete && \
 # Ensure permissions for updating for users not present in /etc/passwd
 # https://blog.openshift.com/jupyter-on-openshift-part-6-running-as-an-assigned-user-id/
     chmod a+w /etc/passwd

Dockerfile.tools

@@ -12,8 +12,14 @@ RUN mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \
     /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate \
     --tooldir=/usr/local --tools --toolconf /"$tool".yaml && \
     cd /usr/local && \ 
-    /usr/local/share/bcbio-nextgen/anaconda/bin/conda clean --yes --tarballs && \
+    /usr/local/share/bcbio-nextgen/anaconda/bin/conda clean -afy && \
     /usr/local/share/bcbio-nextgen/anaconda/bin/conda build purge-all && \
     rm -rf /usr/local/share/bcbio-nextgen/anaconda/pkgs/scipy-0.19.1-np113py27_nomkl_0 && \
     rm -rf /usr/local/share/bcbio-nextgen/anaconda/zulu*.tar.gz && \
-    rm -rf /tmp/bcbio-nextgen-install
+    rm -rf /tmp/bcbio-nextgen-install && \
+    rm -rf bcbio-vc.yaml && \
+    rm -rf bcbio_nextgen_install.py && \
+    rm -rf bcbiotx && \
+    find /usr/local/share/bcbio-nextgen -follow -type f -name "*.pyc" -delete && \
+    find /usr/local/share/bcbio-nextgen -follow -type f -name "*.a" -delete && \
+    find /usr/local/share/bcbio-nextgen -follow -type f -name "*.js.map" -delete 

build_base.sh

@@ -4,7 +4,7 @@ set -ex -o pipefail
 TAG="${BCBIO_VERSION}-${BCBIO_REVISION}"
 
 # build bcbio base
-docker pull ubuntu:16.04
+docker pull ubuntu:18.04
 docker build --no-cache --build-arg "git_revision=${BCBIO_REVISION}" -t "${NS}/bcbio-base:${TAG}" -t "${NS}/bcbio-base:latest" - < Dockerfile.base
 
 # log in to quay.io

packages/bcbio-vc.yaml

@@ -1,5 +1,5 @@
 bio_nextgen:
-- atropos;env=python3
+- atropos
 - bcbio-prioritize
 - bcbio-variation-recall
 - bcftools
@@ -10,7 +10,7 @@ bio_nextgen:
 - bwakit
 - cnvkit
 - coincbc
-- deepvariant;env=dv
+#- deepvariant;env=dv
 - delly
 - duphold
 - extract-sv-reads