diff --git a/README.md b/README.md index cf1d9d3eb0a..7905aff6b02 100644 --- a/README.md +++ b/README.md @@ -74,19 +74,15 @@ releases of the toolkit. docker client, which can be found on the [docker website](https://www.docker.com/get-docker). * Python Dependencies: * GATK4 uses the [Conda](https://conda.io/docs/index.html) package manager to establish and manage the - Python environment and dependencies required by GATK tools that have a Python dependency. There are two different - conda environments that can be used: - * The ```gatk``` environment, which has no special hardware requirements. The GATK Docker image comes with the - "gatk" environment pre-configured. - * The ```gatk-intel``` environment, which requires and uses Intel (AVX2 or AVX-512) hardware acceleration to - increase performance. + Python environment and dependencies required by GATK tools that have a Python dependency. + * The ```gatk``` environment requires and uses Intel hardware acceleration to increase performance (AVX, AVX2 or AVX-512 - + [processors released since Sandy Bridge in 2011 are supported.](https://software.intel.com/en-us/blogs/2018/08/03/intel-optimizations-for-tensorflow-19-now-available) * To establish the conda environment when not using the Docker image, a conda environment must first be "created", and then "activated": * First, make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed (Miniconda is sufficient). * To "create" the conda environment: * If running from a zip or tar distribution, run the command ```conda env create -f gatkcondaenv.yml``` to - create the ```gatk``` environment, or the command ```conda env create -f gatkcondaenv.intel.yml``` to create - the ```gatk-intl``` environment. + create the ```gatk``` environment. * If running from a cloned repository, run ```./gradlew localDevCondaEnv```. This generates the Python package archive and conda yml dependency file(s) in the build directory, and also creates (or updates) the local ```gatk``` conda environment. (To create the ```gatk-intel``` conda environment once the files diff --git a/build.gradle b/build.gradle index 82468828982..57a973e961e 100644 --- a/build.gradle +++ b/build.gradle @@ -77,7 +77,6 @@ final docBuildDir = "$buildDir/docs" final pythonPackageArchiveName = 'gatkPythonPackageArchive.zip' final gatkCondaTemplate = "gatkcondaenv.yml.template" final gatkCondaYML = "gatkcondaenv.yml" -final gatkCondaIntelYML = "gatkcondaenv.intel.yml" final largeResourcesFolder = "src/main/resources/large" final buildPrerequisitesMessage = "See https://github.com/broadinstitute/gatk#building for information on how to build GATK." @@ -479,7 +478,6 @@ task collectBundleIntoDir(type: Copy) { from("$buildDir/$pythonPackageArchiveName") from("$buildDir/$gatkCondaYML") - from("$buildDir/$gatkCondaIntelYML") from("scripts/sv", { into("scripts/sv") }) from("scripts/cnv_wdl/", { into("scripts/cnv_wdl") }) from("scripts/mutect2_wdl/", { into("scripts/mutect2_wdl") }) @@ -520,31 +518,17 @@ task condaStandardEnvironmentDefinition(type: Copy) { include gatkCondaTemplate rename { file -> gatkCondaYML } expand(["condaEnvName":"gatk", - "condaEnvDescription" : "Conda environment for GATK Python Tools", - "tensorFlowDependency" : "tensorflow==$tensorflowVersion"]) + "condaEnvDescription" : "Conda environment for GATK Python Tools"]) doLast { logger.lifecycle("Created standard Conda environment yml file: $gatkCondaYML") } } -task condaIntelEnvironmentDefinition(type: Copy) { - from "scripts" - into buildDir - include gatkCondaTemplate - rename { file -> gatkCondaIntelYML } - expand(["condaEnvName":"gatk-intel", - "condaEnvDescription" : "Conda environment for GATK Python Tools running with Intel hardware acceleration", - "tensorFlowDependency" : - "https://anaconda.org/intel/tensorflow/$tensorflowVersion/download/tensorflow-$tensorflowVersion-cp36-cp36m-linux_x86_64.whl"]) - doLast { - logger.lifecycle("Created Intel Conda environment yml file: $gatkCondaIntelYML") - } -} -// Create two GATK conda environment yml files from the conda enc template -// (one for standard GATK and one for running GATK with Intel hardware). +// Create a GATK conda environment yml file from the conda enc template +// (used TensorFlow with Intel hardware acceleration). task condaEnvironmentDefinition() { - dependsOn 'pythonPackageArchive', 'condaStandardEnvironmentDefinition', 'condaIntelEnvironmentDefinition' + dependsOn 'pythonPackageArchive', 'condaStandardEnvironmentDefinition' } // Create the Python package archive file diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template index 287756a0e9e..837e4bfb2ca 100644 --- a/scripts/gatkcondaenv.yml.template +++ b/scripts/gatkcondaenv.yml.template @@ -14,6 +14,8 @@ dependencies: - readline=6.2=2 - setuptools=36.4.0=py36_1 - sqlite=3.13.0=0 +- tensorflow=1.9.0 +- tensorflow-base=1.9.0 - tk=8.5.18=0 - wheel=0.29.0=py36_0 - xz=5.2.3=0 @@ -43,7 +45,6 @@ dependencies: - scikit-learn==0.19.1 - scipy==1.0.0 - six==1.11.0 - - $tensorFlowDependency - tensorflow-tensorboard==0.4.0rc3 - theano==0.9.0 - tqdm==4.19.4