New: gvcfgenotyper for joint calling with Illumina strelka2

recipes/gvcfgenotyper/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+set -eu -o pipefail
+
+cd external/htslib-*
+./configure --prefix=${PREFIX} --disable-lzma --disable-bz2
+cd ../..
+sed -i.bak 's^-Isrc/c/^-Isrc/c/ -I${PREFIX}/include^' Makefile
+sed -i.bak 's^-lpthread^-lpthread -L$(PREFIX)/lib^' Makefile
+make
+mkdir -p $PREFIX/bin
+cp bin/gvcfgenotyper $PREFIX/bin

recipes/gvcfgenotyper/meta.yaml

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+{% set version="2018.10.15" %}
+{% set hash="e873f57a4df61f24901f2bb2cdf827e1cfcfc663858e56548374b0667d4c9549" %}
+
+package:
+  name: gvcfgenotyper
+  version: {{ version }}
+
+
+source:
+  url: https://github.com/Illumina/gvcfgenotyper/archive/{{ version }}.tar.gz
+  sha256: {{ hash }}
+
+build:
+  number: 0
+  skip: True # [not linux]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+  run:
+    - zlib
+
+test:
+  commands:
+    - gvcfgenotyper 2>&1 | grep 'About:'
+
+about:
+  home: https://github.com/Illumina/gvcfgenotyper
+  license: Apache 2.0
+  summary: A utility for merging and genotyping Illumina-style GVCFs.