From 2156d60acd27895e2a5457ec020a337bdb895428 Mon Sep 17 00:00:00 2001
From: Torsten Seemann <torsten.seemann@gmail.com>
Date: Wed, 2 Oct 2019 10:53:32 +1000
Subject: [PATCH] pirate 1.0.2

---
 recipes/pirate/build.sh  |  4 ++++
 recipes/pirate/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 53 insertions(+)
 create mode 100644 recipes/pirate/build.sh
 create mode 100644 recipes/pirate/meta.yaml

diff --git a/recipes/pirate/build.sh b/recipes/pirate/build.sh
new file mode 100644
index 0000000000000..edf237e90c0cc
--- /dev/null
+++ b/recipes/pirate/build.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+set -eu -o pipefail
+
+mv bin test tools scripts "$PREFIX/"
diff --git a/recipes/pirate/meta.yaml b/recipes/pirate/meta.yaml
new file mode 100644
index 0000000000000..c3813b6b2c705
--- /dev/null
+++ b/recipes/pirate/meta.yaml
@@ -0,0 +1,49 @@
+{% set name = "PIRATE" %}
+{% set version = "1.0.2" %}
+{% set sha256 = "4295f0c3380f1df58fb10792ee8e031c5521e449a6d4e4d289bd8cbf493b33d8" %}
+{% set user = "SionBayliss" %}
+  
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/{{ user }}/{{ name }}/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  noarch: generic
+
+requirements:
+  run:
+    - perl-bioperl >=1.7.2
+    - mcl >=14.137
+    - mafft >=7.310
+    - cd-hit >=4.7
+    - fasttree >=2.1.10
+    - blast >=2.2.31
+    - diamond >=0.9.14
+    - parallel >=20170422
+    - r-ggplot2 >=2.2.1
+    - r-dplyr >=0.7.0
+    - r-phangorn >=2.2.0
+    - bioconductor-ggtree >=1.14.4
+    - unzip
+
+test:
+  commands:
+    - {{ name }} -v | grep '{{ version }}'
+    - {{ name }} -h | grep 'pangenome'
+    - {{ name }} --check
+    
+about:
+  home: https://github.com/{{ user }}/{{ name }}
+  license: GPL3
+  license_file: LICENSE
+  summary: Pangenome analysis and threshold evaluation toolbox
+
+extra:
+  identifiers:
+    - biotools:{{ name|lower }}
+    - doi:10.1101/598391