From 9513921360127be49923e4ab4910111d68a14a14 Mon Sep 17 00:00:00 2001
From: Ryan Raaum <ryan.raaum@lehman.cuny.edu>
Date: Wed, 3 Oct 2018 12:12:10 -0400
Subject: [PATCH 1/4] New recipe for RFMix

---
 recipes/rfmix/build.sh  | 11 +++++++++++
 recipes/rfmix/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 recipes/rfmix/build.sh
 create mode 100644 recipes/rfmix/meta.yaml

diff --git a/recipes/rfmix/build.sh b/recipes/rfmix/build.sh
new file mode 100644
index 0000000000000..5d7ca4a00d0e2
--- /dev/null
+++ b/recipes/rfmix/build.sh
@@ -0,0 +1,11 @@
+# following full suggested build path of rfmix
+aclocal                      # creates aclocal.m4
+autoheader                   # creates config.h.in
+autoconf                     # creates configure
+automake --add-missing       # creates Makefile.in
+./configure                  # generates the Makefile
+make
+
+# Install
+mkdir -p $PREFIX/bin
+cp {rfmix,simulate} $PREFIX/bin/
\ No newline at end of file
diff --git a/recipes/rfmix/meta.yaml b/recipes/rfmix/meta.yaml
new file mode 100644
index 0000000000000..2b7c33bd1a75d
--- /dev/null
+++ b/recipes/rfmix/meta.yaml
@@ -0,0 +1,36 @@
+package:
+  name: rfmix
+  version: '2.9505bfa'
+
+source:
+  url: https://github.com/slowkoni/rfmix/archive/9505bfae51ea57314d98060e6d09f6759cda8e8d.zip
+  sha256: f15a8fe9bc8e06579f96c727dd91ca07b726e9bde305ce0d8d4ee233b1b299af
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+  host:
+    - pthread-stubs
+  run:
+    - pthread-stubs
+
+about:
+  home: https://github.com/slowkoni/rfmix
+  license: Free for Academic Use
+  summary: 'RFMix implements a fast discriminative approach to modeling ancestry along an admixed chromosome given observed haplotype sequences of known or inferred ancestry.'
+
+test:
+  commands:
+    - rfmix --help > /dev/null 2>&1
+    - simulate --help > /dev/null 2>&1
+
+extra:
+  identifiers:
+    - biotools:RFMix
+    - doi:10.1016/j.ajhg.2013.06.020

From 19faeb1cb461c7b0b10ac5a42cae25232c5639c1 Mon Sep 17 00:00:00 2001
From: Ryan Raaum <ryan.raaum@lehman.cuny.edu>
Date: Wed, 3 Oct 2018 14:15:19 -0400
Subject: [PATCH 2/4] updated version number information

---
 recipes/rfmix/meta.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/recipes/rfmix/meta.yaml b/recipes/rfmix/meta.yaml
index 2b7c33bd1a75d..c42de230bcf65 100644
--- a/recipes/rfmix/meta.yaml
+++ b/recipes/rfmix/meta.yaml
@@ -1,6 +1,8 @@
 package:
   name: rfmix
-  version: '2.9505bfa'
+  # Version number in github for this recipe is 2.03-r0, but there are no release tarballs. 
+  # To ensure stability, this recipe links to the git commit with prefix '9505bfa'
+  version: '2.03-r0.9505bfa'
 
 source:
   url: https://github.com/slowkoni/rfmix/archive/9505bfae51ea57314d98060e6d09f6759cda8e8d.zip

From 0b321b388c4f007044b4b8586caea1d236aaee72 Mon Sep 17 00:00:00 2001
From: Ryan Raaum <ryan.raaum@lehman.cuny.edu>
Date: Wed, 3 Oct 2018 14:16:44 -0400
Subject: [PATCH 3/4] updated version number information

---
 recipes/rfmix/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/rfmix/meta.yaml b/recipes/rfmix/meta.yaml
index c42de230bcf65..c8208a9e91103 100644
--- a/recipes/rfmix/meta.yaml
+++ b/recipes/rfmix/meta.yaml
@@ -2,7 +2,7 @@ package:
   name: rfmix
   # Version number in github for this recipe is 2.03-r0, but there are no release tarballs. 
   # To ensure stability, this recipe links to the git commit with prefix '9505bfa'
-  version: '2.03-r0.9505bfa'
+  version: '2.03-r0-9505bfa'
 
 source:
   url: https://github.com/slowkoni/rfmix/archive/9505bfae51ea57314d98060e6d09f6759cda8e8d.zip

From cc8c9518fa9fb637e35607407b5e410cee2991b6 Mon Sep 17 00:00:00 2001
From: Ryan Raaum <ryan.raaum@lehman.cuny.edu>
Date: Wed, 3 Oct 2018 14:31:54 -0400
Subject: [PATCH 4/4] updated version number information

---
 recipes/rfmix/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/rfmix/meta.yaml b/recipes/rfmix/meta.yaml
index c8208a9e91103..f5c70ed4a56fa 100644
--- a/recipes/rfmix/meta.yaml
+++ b/recipes/rfmix/meta.yaml
@@ -2,7 +2,8 @@ package:
   name: rfmix
   # Version number in github for this recipe is 2.03-r0, but there are no release tarballs. 
   # To ensure stability, this recipe links to the git commit with prefix '9505bfa'
-  version: '2.03-r0-9505bfa'
+  # Also, dash in version number replaced with dot to pass conda linting specifications.
+  version: '2.03.r0.9505bfa'
 
 source:
   url: https://github.com/slowkoni/rfmix/archive/9505bfae51ea57314d98060e6d09f6759cda8e8d.zip