conda change for tensorflow with intel speedups (#5725)

build.gradle

@@ -64,7 +64,6 @@ final barclayVersion = System.getProperty('barclay.version','2.1.0')
 final sparkVersion = System.getProperty('spark.version', '2.2.0')
 final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
 final disqVersion = System.getProperty('disq.version','0.2.0')
-final tensorflowVersion = System.getProperty('tensorflow.version','1.9.0')
 final genomicsdbVersion = System.getProperty('genomicsdb.version','1.0.0-rc2')
 final testNGVersion = '6.11'
 // Using the shaded version to avoid conflicts between its protobuf dependency
@@ -519,8 +518,7 @@ task condaStandardEnvironmentDefinition(type: Copy) {
     include gatkCondaTemplate
     rename { file -> gatkCondaYML }
     expand(["condaEnvName":"gatk",
-            "condaEnvDescription" : "Conda environment for GATK Python Tools",
-            "tensorFlowDependency" : "tensorflow==$tensorflowVersion"])
+            "condaEnvDescription" : "Conda environment for GATK Python Tools"])
     doLast {
         logger.lifecycle("Created standard Conda environment yml file: $gatkCondaYML")
     }

scripts/gatkcondaenv.yml.template

@@ -15,6 +15,7 @@ dependencies:
 - readline=6.2=2
 - setuptools=36.4.0=py36_1
 - sqlite=3.13.0=0
+- anaconda::tensorflow=1.12.0=mkl_py36h69b6ba0_0
 - tk=8.5.18=0
 - wheel=0.29.0=py36_0
 - xz=5.2.3=0
@@ -32,7 +33,7 @@ dependencies:
   - matplotlib==2.1.0
   - pandas==0.21.0
   - patsy==0.4.1
-  - protobuf==3.5.0.post1
+  - protobuf==3.6.1
   - pymc3==3.1
   - pyparsing==2.2.0
   - pysam==0.13
@@ -43,7 +44,6 @@ dependencies:
   - scikit-learn==0.19.1
   - scipy==1.0.0
   - six==1.11.0
-  - $tensorFlowDependency
   - theano==1.0.4
   - tqdm==4.19.4
   - werkzeug==0.12.2