Update: gatk4 (4.0.9.0), vqsr_cnn (0.0.194), duphold (0.0.6) (#11057)

* Update: gatk4 (4.0.9.0), vqsr_cnn (0.0.194), duphold (0.0.6)

- gatk4 with MuTect2 fixes
- duphold with fixes for variant at start of chromosome brentp/duphold#3

* vqsr_cnn: add new gatktool dependency

recipes/duphold/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "duphold" %}
-{% set version = "0.0.3" %}
-{% set sha256hash = "956078be7b3d618f4092bf71b5da5fafbe335ccbe40070ceced3bd80fb5b5ac8" %}
+{% set version = "0.0.6" %}
+{% set sha256hash = "6bf68965393306e322afdf171da813e3fb331ca2a47226d6ab70e92fe6c7e523" %}
 
 package:
   name: {{ name|lower }}

recipes/gatk4/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "4.0.8.1" %}
-{% set sha256 = "e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9" %}
+{% set version = "4.0.9.0" %}
+{% set sha256 = "c5fbfbb4feea45a33e212f5168d30f62ab118c77f18f2bd376c8b593089c6027" %}
 
 package:
   name: gatk4

recipes/gatktool/meta.yaml

@@ -0,0 +1,32 @@
+{% set name = "gatktool" %}
+{% set version = "0.0.1" %}
+{% set hash_value = "6c672e4c901c58d2c8dca872c186c1ea22867f6aa4580c89546ad65faf43fecf" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: '{{ hash_value }}'
+
+build:
+  noarch: python
+  number: 0
+  script: python -m pip install --no-deps --ignore-installed .
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+
+test:
+  imports:
+    - gatktool
+
+about:
+  home: https://broadinstitute.org/
+  license: MIT
+  summary: Functions and classes used to extend a GATK tool with Python

recipes/vqsr_cnn/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "vqsr_cnn" %}
-{% set version = "0.0.132" %}
-{% set hash_value = "f82d0389a58a993ea7ff3c3094a75a51326c37023d4f24aad18343ab11dce721" %}
+{% set version = "0.0.194" %}
+{% set hash_value = "03ee84a1e9a31a45635409c5fb8ad82178586e016cd7cfc51737e722311fee68" %}
 
 package:
   name: '{{ name|lower }}'
@@ -12,13 +12,14 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   script: python -m pip install --no-deps --ignore-installed .
 
 requirements:
   host:
     - python
     - pip
+    - gatktool
     - tensorflow
     - keras >=2.0
     - numpy >=1.13.1
@@ -30,6 +31,7 @@ requirements:
     - biopython >=1.70
   run:
     - python
+    - gatktool
     - tensorflow
     - keras >=2.0
     - numpy >=1.13.1