Update: deepvariant 0.7.2 model and dependencies

recipes/deepvariant/dv_make_examples.py

@@ -33,7 +33,7 @@ def main():
     parser.add_argument("--sample", required=True, help="Sample name")
     parser.add_argument("--ref", required=True, help="Reference genome")
     parser.add_argument("--reads", required=True, help="Input BAM file")
-    parser.add_argument("--regions", required=True, help="Genomic region to process")
+    parser.add_argument("--regions", help="Genomic region to process")
     parser.add_argument("--logdir", required=True)
     parser.add_argument("--examples", required=True, help="Output directory for examples")
     parser.add_argument("-h", "--help", action=DVHelp)
@@ -45,10 +45,11 @@ def main():
     lib_path = os.path.join(os.path.dirname(conda_path), "lib")
     py_exe = sys.executable
     split_inputs = " ".join(str(x) for x in range(0, int(args.cores)))
+    regions = ("--regions %s" % args.regions) if args.regions else ""
     cmd = ("export PATH={conda_path}:$PATH && export LD_LIBRARY_PATH={lib_path}:$LD_LIBRARY_PATH && "
            "parallel --eta --halt 2 --joblog {args.logdir}/log --res {args.logdir} "
            "{py_exe} {bin_dir}/make_examples.zip "
-           "--mode calling --ref {args.ref} --reads {args.reads} --regions {args.regions} "
+           "--mode calling --ref {args.ref} --reads {args.reads} {regions} "
            "--examples {args.examples}/{args.sample}.tfrecord@{args.cores}.gz --task {{}} "
            "::: {split_inputs}")
     sys.exit(subprocess.call(cmd.format(**locals()), shell=True))

recipes/deepvariant/meta.yaml

@@ -18,7 +18,7 @@ source:
   url: https://github.com/google/deepvariant/releases/download/v{{ version }}/deepvariant.zip
   sha256: '{{ sha256 }}'
 build:
-  number: 0
+  number: 1
   skip: true  # [osx or not py27]
 
 requirements:
@@ -40,7 +40,7 @@ requirements:
     - htslib
     - numpy
     - curl
-    - tensorflow 1.11.*
+    - tensorflow 1.12.*
     - protobuf
     - contextlib2
     - enum34

recipes/deepvariant/post-link.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -eu -o pipefail
 
-MODEL_VERSION="0.7.0"
+MODEL_VERSION="0.7.2"
 
 GSUTIL=$PREFIX/bin/gsutil
 for MODEL_TYPE in wgs wes