Finishing off things I hope

Dockerfile

@@ -8,7 +8,7 @@ ADD . /gatk
 WORKDIR /gatk
 
 # Get an updated gcloud signing key, in case the one in the base image has expired
-RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add -
+#RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add -
 RUN add-apt-repository universe && apt update
 RUN apt-get --assume-yes install git-lfs
 RUN git lfs install

scripts/docker/gatkbase/Dockerfile

@@ -25,10 +25,11 @@ RUN apt-get update && \
     apt-get -y autoremove
 
 #### Specific for google cloud support
-RUN export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" && \
-    echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
-    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - && \
-    apt-get update -y && apt-get install google-cloud-sdk -y && \
+#RUN export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" && \
+#    echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
+#    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - && \
+
+RUN apt-get update -y && apt-get install google-cloud-sdk -y && \
     apt-get -y autoremove && \
     apt-get -y clean
 ###########

src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf

@@ -1193,7 +1193,7 @@
 20	10006292	.	A	<NON_REF>	.	.	END=10006383	GT:DP:GQ:MIN_DP:PL	./.:81:99:76:0,120,1800	./.:52:99:37:0,99,1162
 20	10006384	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:81:99:76:0,120,1800	./.:43:89:43:0,89,1158
 20	10006385	.	A	<NON_REF>	.	.	END=10006403	GT:DP:GQ:MIN_DP:PL	./.:81:99:76:0,120,1800	./.:45:99:40:0,102,1530
-20	10006404	.	A	C,<NON_REF>	.	.	BaseQRankSum=1.72;ClippingRankSum=0.00;DP=120;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=424251,120;ReadPosRankSum=-5.390e-01	GT:AD:DP:GQ:PL:SB	./.:0,76,1:77:99:2957,228,0,2957,228,2957:0,0,28,49	./.:1,36,0:37:99:1061,100,0,1064,107,1071:0,1,15,21
+20	10006404	.	A	C,<NON_REF>	.	.	BaseQRankSum=1.72;ClippingRankSum=0.00;DP=120;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=424251,120;ReadPosRankSum=-5.390e-01	GT:AD:DP:GQ:PL:SB	./.:0,76,0:76:99:2957,228,0,2957,228,2957:0,0,27,49	./.:1,36,0:37:99:1061,100,0,1064,107,1071:0,1,15,21
 20	10006405	.	C	<NON_REF>	.	.	END=10006410	GT:DP:GQ:MIN_DP:PL	./.:78:99:65:0,120,1800	./.:40:99:38:0,102,1159
 20	10006411	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:78:99:65:0,120,1800	./.:38:80:38:0,80,1080
 20	10006412	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:78:99:65:0,120,1800	./.:38:75:38:0,75,1050