From 1364551de209798bfb2d022fd9403c8d00d07c6b Mon Sep 17 00:00:00 2001
From: Torsten Seemann <torsten.seemann@gmail.com>
Date: Wed, 8 Aug 2018 18:56:22 +1000
Subject: [PATCH] Update snippy to 4.0.0

---
 recipes/snippy/3.2/build.sh  |  3 +++
 recipes/snippy/3.2/meta.yaml | 44 ++++++++++++++++++++++++++++++++++++
 recipes/snippy/build.sh      |  3 ++-
 recipes/snippy/meta.yaml     | 27 +++++++++++++---------
 4 files changed, 65 insertions(+), 12 deletions(-)
 create mode 100755 recipes/snippy/3.2/build.sh
 create mode 100644 recipes/snippy/3.2/meta.yaml

diff --git a/recipes/snippy/3.2/build.sh b/recipes/snippy/3.2/build.sh
new file mode 100755
index 0000000000000..0f4beb390a972
--- /dev/null
+++ b/recipes/snippy/3.2/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+cp -r bin/* $PREFIX/bin
diff --git a/recipes/snippy/3.2/meta.yaml b/recipes/snippy/3.2/meta.yaml
new file mode 100644
index 0000000000000..b20967800279b
--- /dev/null
+++ b/recipes/snippy/3.2/meta.yaml
@@ -0,0 +1,44 @@
+{% set name = "snippy" %}
+{% set version = "3.2" %}
+{% set hash = "75377acc4687e21d46d773936389e3f0abd8441076d3c9acdd31be13b53352a8" %}
+
+package:
+  name: {{ name }}
+  version: "{{ version | replace('-', '_') }}"
+
+source:
+  sha256: {{ hash }}
+  url: https://github.com/tseemann/{{ name }}/archive/v{{ version }}.tar.gz
+
+build:
+  number: 1
+
+requirements:
+  run:
+    - perl
+    - perl-bioperl
+    - perl-list-moreutils
+    - perl-file-slurp
+    - perl-time-piece
+    - bwa >=0.7.12
+    - samtools >=1.3
+    - bcftools >=1.7
+    - parallel >=20130422
+    - freebayes >=1.1
+    - vcflib
+    - vcftools >=0.1.14
+    - snpeff >=4.3
+
+test:
+  commands:
+  - snippy --version
+  - snippy --check
+
+about:
+  home: https://github.com/tseemann/snippy
+  license: GPL2
+  summary: Rapid bacterial SNP calling and core genome alignments
+
+extra:
+  identifiers:
+    - biotools:snippy
diff --git a/recipes/snippy/build.sh b/recipes/snippy/build.sh
index 0f4beb390a972..54fa18a3db6d4 100755
--- a/recipes/snippy/build.sh
+++ b/recipes/snippy/build.sh
@@ -1,3 +1,4 @@
 #!/bin/bash
 
-cp -r bin/* $PREFIX/bin
+rm -f binaries/{darwin,linux}/*
+cp -r * $PREFIX/
diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml
index b20967800279b..78f64f60f6ae1 100644
--- a/recipes/snippy/meta.yaml
+++ b/recipes/snippy/meta.yaml
@@ -1,10 +1,10 @@
 {% set name = "snippy" %}
-{% set version = "3.2" %}
-{% set hash = "75377acc4687e21d46d773936389e3f0abd8441076d3c9acdd31be13b53352a8" %}
+{% set version = "4.0.0" %}
+{% set hash = "ccc3839276e8ae9d1807e975803c3593504521f2cd011dfdbcc249b8abf17700" %}
 
 package:
   name: {{ name }}
-  version: "{{ version | replace('-', '_') }}"
+  version: "{{ version }}"
 
 source:
   sha256: {{ hash }}
@@ -12,27 +12,32 @@ source:
 
 build:
   number: 1
+  skip: True # [osx]
 
 requirements:
   run:
     - perl
     - perl-bioperl
     - perl-list-moreutils
-    - perl-file-slurp
     - perl-time-piece
-    - bwa >=0.7.12
-    - samtools >=1.3
-    - bcftools >=1.7
-    - parallel >=20130422
+    - bwa >=0.7.17
+    - samtools >=1.8
+    - bcftools >=1.8
+    - parallel >=20170422
     - freebayes >=1.1
     - vcflib
-    - vcftools >=0.1.14
     - snpeff >=4.3
+    - vt >=0.5772
+    - snp-sites >=2.4
+    - emboss >=6.0
+    - samclip >=0.2
+    - seqtk >=1.2
+    - minimap2 >=2.10
 
 test:
   commands:
-  - snippy --version
-  - snippy --check
+    - snippy --version
+    - snippy --check
 
 about:
   home: https://github.com/tseemann/snippy