diff --git a/recipes/deepvariant/dv_make_examples.py b/recipes/deepvariant/dv_make_examples.py index 60168c946d0d4..26707900fb7d8 100644 --- a/recipes/deepvariant/dv_make_examples.py +++ b/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)) diff --git a/recipes/deepvariant/meta.yaml b/recipes/deepvariant/meta.yaml index 4c1c642931682..86f1c1485585b 100644 --- a/recipes/deepvariant/meta.yaml +++ b/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 diff --git a/recipes/deepvariant/post-link.sh b/recipes/deepvariant/post-link.sh index f7174d35d94d9..650637bb1b564 100644 --- a/recipes/deepvariant/post-link.sh +++ b/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