From b7f1ecbfac236cf69fdd54b5da411ba103a0df62 Mon Sep 17 00:00:00 2001
From: Salvatore Cosentino <salvoc81@users.noreply.github.com>
Date: Thu, 18 Oct 2018 09:30:41 +0900
Subject: [PATCH] Added recipe for SonicParanoid 1.0.13 (#11271)

* Added recipe for SonicParanoid 1.0.13

* removed 'x.x' for numpy, added basic test

* fixed linter related errors

* compiler set to cxx and added host section (same build error!)

* removed host section

* moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md

* removed build: noarch

* added build and extra sections

* set build number to 0; removed skip build; added python3 minimum version; added test for all executables.

* restored sh python module as requirement

* added Make to run; updated release to latest commit

* remove c compiler from meta.yaml

* modified build.sh to compile source codel added make in build section

* updated to latest commit

* updated to latest version with make included in setup.py

* reverted build.sh to the simplest version (python setup.py install)
---
 recipes/sonicparanoid/build.sh  |  1 +
 recipes/sonicparanoid/meta.yaml | 52 +++++++++++++++++++++++++++++++++
 2 files changed, 53 insertions(+)
 create mode 100644 recipes/sonicparanoid/build.sh
 create mode 100644 recipes/sonicparanoid/meta.yaml

diff --git a/recipes/sonicparanoid/build.sh b/recipes/sonicparanoid/build.sh
new file mode 100644
index 0000000000000..f9fb4ea80ce91
--- /dev/null
+++ b/recipes/sonicparanoid/build.sh
@@ -0,0 +1 @@
+python setup.py install --single-version-externally-managed --record=record.txt  # Python command to install the script.
diff --git a/recipes/sonicparanoid/meta.yaml b/recipes/sonicparanoid/meta.yaml
new file mode 100644
index 0000000000000..928d9dfcccf8e
--- /dev/null
+++ b/recipes/sonicparanoid/meta.yaml
@@ -0,0 +1,52 @@
+{% set name = "sonicparanoid" %}
+{% set version = "1.0.13" %}
+{% set commit = "2adfc811f035" %}
+
+build:
+  number: 0
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: https://bitbucket.org/salvocos/sonicparanoid/get/{{ commit }}.zip
+  sha256: c8ee657132e3da08c4c5e225514da99eccfe3902089157aed2e873eee552ac05
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+  host:
+    - make
+    - python >=3.5
+    - numpy
+    - cython
+  run:
+    - make
+    - python >=3.5
+    - pip >=9.0.1
+    - cython >=0.27.0
+    - setuptools >=24.2.0
+    - biopython >=1.67
+    - pandas >=0.22.0
+    - numpy >=1.13.0
+    - sh >=1.12.14
+
+test:
+  commands:
+    - "sonicparanoid"
+    - "sonicparanoid-get-mmseqs2 --help"
+    - "sonicparanoid-set-mmseqs2 --help"
+    - "sonicparanoid-get-test-data --help"
+    - "sonicparanoid-extract --help"
+
+about:
+  home: "http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid/"
+  license: "GNU General Public License v3"
+  license_family: "GPL3"
+  license_file: "LICENSE.md"
+  summary: "SonicParanoid: fast, easy and accurate orthology inference"
+
+extra:
+  identifiers:
+    - https://doi.org/10.1093/bioinformatics/bty631