From 98f1d29cee2279586a94ab8e8e1adea868001965 Mon Sep 17 00:00:00 2001
From: Torsten Seemann <tseemann@users.noreply.github.com>
Date: Sat, 4 Aug 2018 15:22:14 +1000
Subject: [PATCH] Update vt to 0.57721 (#10253)

---
 recipes/vt/2015.11.10/build.sh  | 14 ++++++++++++++
 recipes/vt/2015.11.10/meta.yaml | 28 ++++++++++++++++++++++++++++
 recipes/vt/build.sh             |  3 ++-
 recipes/vt/meta.yaml            | 25 ++++++++++++++++++-------
 4 files changed, 62 insertions(+), 8 deletions(-)
 create mode 100644 recipes/vt/2015.11.10/build.sh
 create mode 100644 recipes/vt/2015.11.10/meta.yaml

diff --git a/recipes/vt/2015.11.10/build.sh b/recipes/vt/2015.11.10/build.sh
new file mode 100644
index 0000000000000..22bbe965baf75
--- /dev/null
+++ b/recipes/vt/2015.11.10/build.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+
+export CFLAGS="-I$PREFIX/include"
+export CPATH=${PREFIX}/include
+export LDFLAGS="-L${PREFIX}/lib"
+export CPPFLAGS="-I${PREFIX}/include"
+
+make
+mkdir -p $PREFIX/bin
+cp vt $PREFIX/bin
diff --git a/recipes/vt/2015.11.10/meta.yaml b/recipes/vt/2015.11.10/meta.yaml
new file mode 100644
index 0000000000000..c772c054ac50f
--- /dev/null
+++ b/recipes/vt/2015.11.10/meta.yaml
@@ -0,0 +1,28 @@
+package:
+  name: vt
+  version: '2015.11.10'
+
+source:
+  url: https://github.com/atks/vt/archive/15f90de5.tar.gz
+  sha256: a135be9a9b3094e21e92e915633e114a794d197172093fcab4c0999b97fa7e87
+
+build:
+  number: 3
+  skip: True # [osx]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+  run:
+    - zlib
+
+test:
+  commands:
+    - vt
+
+about:
+  home: https://github.com/atks/vt
+  license: MIT
+  summary: A tool set for short variant discovery in genetic sequence data
diff --git a/recipes/vt/build.sh b/recipes/vt/build.sh
index 22bbe965baf75..2c9ec0f2ecd7d 100644
--- a/recipes/vt/build.sh
+++ b/recipes/vt/build.sh
@@ -9,6 +9,7 @@ export CPATH=${PREFIX}/include
 export LDFLAGS="-L${PREFIX}/lib"
 export CPPFLAGS="-I${PREFIX}/include"
 
-make
+make -j${CPU_COUNT}
+make test
 mkdir -p $PREFIX/bin
 cp vt $PREFIX/bin
diff --git a/recipes/vt/meta.yaml b/recipes/vt/meta.yaml
index c772c054ac50f..c0b75f1e2d1b1 100644
--- a/recipes/vt/meta.yaml
+++ b/recipes/vt/meta.yaml
@@ -1,28 +1,39 @@
+{% set name = "vt" %}
+{% set version = "0.57721" %}
+
 package:
-  name: vt
-  version: '2015.11.10'
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://github.com/atks/vt/archive/15f90de5.tar.gz
-  sha256: a135be9a9b3094e21e92e915633e114a794d197172093fcab4c0999b97fa7e87
+  url: https://github.com/atks/{{ name }}/archive/{{ version }}.tar.gz
+  sha256: 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17
 
 build:
-  number: 3
+  number: 0
   skip: True # [osx]
 
 requirements:
   build:
     - {{ compiler('cxx') }}
   host:
+    - bzip2
+    - curl
+    - xz
     - zlib
+    - libdeflate
   run:
+    - bzip2
+    - curl
+    - xz
     - zlib
+    - libdeflate
 
 test:
   commands:
     - vt
 
 about:
-  home: https://github.com/atks/vt
+  home: https://genome.sph.umich.edu/wiki/Vt
   license: MIT
-  summary: A tool set for short variant discovery in genetic sequence data
+  summary: A tool set for manipulating and generating VCF files