done (#828)

docker/jupyter/user-scripts/install_gatk_cnn.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+apt-get install -yq --no-install-recommends \
+    certifi=2016.2.28=py36_0 \
+    intel-openmp=2018.0.0 \
+    mkl=2018.0.1 \
+    mkl-service=1.1.2 \
+    readline=6.2=2 \
+    setuptools=36.4.0=py36_1 \
+    sqlite=3.13.0=0 \
+    tk=8.5.18=0 \
+    wheel=0.29.0=py36_0 \
+    xz=5.2.3=0 \
+    zlib=1.2.11=0
+
+pip3 install biopython==1.70
+pip3 install bleach==1.5.0
+pip3 install cycler==0.10.0
+pip3 install enum34==1.1.6
+pip3 install h5py==2.7.1
+pip3 install html5lib==0.9999999
+pip3 install joblib==0.11
+pip3 install keras==2.2.0
+pip3 install markdown==2.6.9
+pip3 install matplotlib==2.1.0
+pip3 install numpy==1.13.3
+pip3 install pandas==0.21.0
+pip3 install patsy==0.4.1
+pip3 install protobuf==3.5.0.post1
+pip3 install pymc3==3.1
+pip3 install pyparsing==2.2.0
+pip3 install pysam==0.13
+pip3 install python-dateutil==2.6.1
+pip3 install pytz==2017.3
+pip3 install pyvcf==0.6.8
+pip3 install pyyaml==3.12
+pip3 install scikit-learn==0.19.1
+pip3 install scipy==1.0.0
+pip3 install six==1.11.0
+pip3 install tensorflow==1.9.0
+pip3 install theano==0.9.0
+pip3 install tqdm==4.19.4
+pip3 install werkzeug==0.12.2
+
+set -e
+GATK_VERSION=4.1.0.0
+GATK_ZIP_PATH=/tmp/gatk-$GATK_VERSION.zip
+
+#download the gatk zip if it doesn't already exist
+if ! [ -f $GATK_ZIP_PATH ]; then
+  # curl and follow redirects and output to a temp file
+  curl -L -o $GATK_ZIP_PATH https://github.com/broadinstitute/gatk/releases/download/$GATK_VERSION/gatk-$GATK_VERSION.zip
+fi
+
+# unzip with forced overwrite (if necessary) to /bin
+unzip -o $GATK_ZIP_PATH -d /etc/
+
+# make a symlink to gatk right inside bin so it's available from the existing PATH
+ln -s /etc/gatk-$GATK_VERSION/gatk /bin/gatk
+
+pip3 install /etc/gatk-$GATK_VERSION/gatkPythonPackageArchive.zip
+