From c86a4c616d73a73a914517c6d3bbd4823a756e0b Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 6 Nov 2024 13:06:43 -0800
Subject: [PATCH 01/15] bump/finemap

---
 recipes/finemap/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index c16f675ebd1df..ad93eed496d5b 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -5,17 +5,17 @@
 
 package:
   name: finemap
-  version: 1.4.1
+  version: 1.4.2
 source:
-  sha256: 75c919d9cc981bc08e1a982b1632110109ffe6a057e803c9aa36c143aa56d546
-  url: http://www.christianbenner.com/finemap_v1.4.1_x86_64.tgz
+  sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9
+  url: http://www.christianbenner.com/finemap_v1.4.2_x86_64.tgz
 build:
   binary_relocation: false
   noarch: generic
   number: '0'
   script:
     - install -Dd ${PREFIX}/bin
-    - install -D -m 755 finemap_v1.4.1_x86_64 ${PREFIX}/bin/finemap
+    - install -D -m 755 finemap_v1.4.2_x86_64 ${PREFIX}/bin/finemap
   string: '0'
 requirements:
   build: []

From 915d4f3298dd4755e4860d0e1bbb82417052341f Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 6 Nov 2024 13:11:13 -0800
Subject: [PATCH 02/15] add run_exports to FINEMAP recipe

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

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index ad93eed496d5b..1fb9fb143cb3f 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -17,6 +17,8 @@ build:
     - install -Dd ${PREFIX}/bin
     - install -D -m 755 finemap_v1.4.2_x86_64 ${PREFIX}/bin/finemap
   string: '0'
+  run_exports:
+    - {{ pin_subpackage('finemap', max_pin="x") }}
 requirements:
   build: []
   host: []

From ed0ade2607a195d80f8a8ae6955b503c966d2e7b Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 8 Nov 2024 14:17:00 -0800
Subject: [PATCH 03/15] add script and build info

---
 recipes/finemap/meta.yaml | 39 +++++++++++++++++++--------------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 1fb9fb143cb3f..5aec60b90f12b 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -1,39 +1,38 @@
-# This file created by conda-build 3.22.0
-# meta.yaml template originally from:
-# /home/conda/conda-forge/recipes/finemap, last modified Thu Oct 20 22:53:08 2022
-# ------------------------------------------------
+{% set name = "finemap" %}
+{% set version = "1.4.2" %}
 
 package:
-  name: finemap
-  version: 1.4.2
+  name: {{ name }}
+  version: {{ version }}
+
 source:
-  sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9
-  url: http://www.christianbenner.com/finemap_v1.4.2_x86_64.tgz
+  url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux]
+  sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux]
+
 build:
-  binary_relocation: false
-  noarch: generic
-  number: '0'
-  script:
-    - install -Dd ${PREFIX}/bin
-    - install -D -m 755 finemap_v1.4.2_x86_64 ${PREFIX}/bin/finemap
-  string: '0'
+  number: 0
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
+  script:
+    - mkdir -p ${PREFIX}/bin
+    - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux]
+
 requirements:
   build: []
   host: []
   run: []
+
 test:
   commands:
-    - test -f $PREFIX/bin/finemap
+    - finemap --help
+
 about:
   home: http://www.christianbenner.com
   license: Other
   license_file: LICENSE
-  summary: Program for identifying causal SNPs and their effect sizes and heritability
-    contributions
+  summary: >
+    Program for identifying causal SNPs and their effect sizes and heritability contributions
+
 extra:
-  copy_test_source_files: true
-  final: true
   recipe-maintainers:
     - danielnachun

From 8a0e78408e78417d806fa38f05e4a920bac5fd95 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 8 Nov 2024 14:42:00 -0800
Subject: [PATCH 04/15] include compiler since this package is not noarch

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

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 5aec60b90f12b..1b868ad5dd74b 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -18,7 +18,8 @@ build:
     - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux]
 
 requirements:
-  build: []
+  build:
+    - {{ compiler('cxx') }}
   host: []
   run: []
 

From f6e4b0722c7aea2b7f379672fa31cd8e31110405 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 8 Nov 2024 15:04:01 -0800
Subject: [PATCH 05/15] only build on linux

---
 recipes/finemap/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 1b868ad5dd74b..4613707ffbabd 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -11,6 +11,7 @@ source:
 
 build:
   number: 0
+  skip: True # [not linux]
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
   script:

From f9bee23ff1427f5a64a429c4271684bb18f3ecc4 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 8 Nov 2024 15:28:42 -0800
Subject: [PATCH 06/15] add outline for osx

hopefully someone more knowledgeable than me will be able to figure out how to make osx work too

The osx build is unable to find shared libraries. I tried using install_name_tool to replace the paths to the libraries, but I couldn't get it to work
---
 recipes/finemap/meta.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 4613707ffbabd..3cbcd36fac434 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -8,15 +8,19 @@ package:
 source:
   url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux]
   sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux]
+  url: http://www.christianbenner.com/finemap_v{{ version }}_MacOSX.tgz # [osx]
+  sha256: e2967e5586347a8ac5cbcddf3c0e41bf8d3e7793875f78b509d07903d17a415b # [osx]
 
 build:
   number: 0
+  # skip broken osx for now
   skip: True # [not linux]
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
   script:
     - mkdir -p ${PREFIX}/bin
     - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux]
+    - install -m 755 finemap_v{{ version }}_MacOSX ${PREFIX}/bin/finemap # [osx]
 
 requirements:
   build:

From 21fac97f0b54320a10899bc03834f59b29b22627 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 8 Nov 2024 21:29:01 -0800
Subject: [PATCH 07/15] add suggestions from PR review

Thanks, Martin!
---
 recipes/finemap/meta.yaml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 3cbcd36fac434..e082b0d2c8e8e 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -6,10 +6,10 @@ package:
   version: {{ version }}
 
 source:
-  url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux]
-  sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux]
-  url: http://www.christianbenner.com/finemap_v{{ version }}_MacOSX.tgz # [osx]
-  sha256: e2967e5586347a8ac5cbcddf3c0e41bf8d3e7793875f78b509d07903d17a415b # [osx]
+  - url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux]
+    sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux]
+  - url: http://www.christianbenner.com/finemap_v{{ version }}_MacOSX.tgz # [osx]
+    sha256: e2967e5586347a8ac5cbcddf3c0e41bf8d3e7793875f78b509d07903d17a415b # [osx]
 
 build:
   number: 0
@@ -23,8 +23,7 @@ build:
     - install -m 755 finemap_v{{ version }}_MacOSX ${PREFIX}/bin/finemap # [osx]
 
 requirements:
-  build:
-    - {{ compiler('cxx') }}
+  build: []
   host: []
   run: []
 

From f6d3bca22857bb7ed44acba047dd2c2d0ce78ba8 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 11 Nov 2024 12:54:03 -0800
Subject: [PATCH 08/15] skip building finemap if not linux64

---
 recipes/finemap/meta.yaml | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index e082b0d2c8e8e..0a8756c5dd17c 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -6,15 +6,15 @@ package:
   version: {{ version }}
 
 source:
-  - url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux]
-    sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux]
+  - url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux64]
+    sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux64]
   - url: http://www.christianbenner.com/finemap_v{{ version }}_MacOSX.tgz # [osx]
     sha256: e2967e5586347a8ac5cbcddf3c0e41bf8d3e7793875f78b509d07903d17a415b # [osx]
 
 build:
   number: 0
   # skip broken osx for now
-  skip: True # [not linux]
+  skip: True # [not linux64]
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
   script:
@@ -22,11 +22,6 @@ build:
     - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux]
     - install -m 755 finemap_v{{ version }}_MacOSX ${PREFIX}/bin/finemap # [osx]
 
-requirements:
-  build: []
-  host: []
-  run: []
-
 test:
   commands:
     - finemap --help

From 7519e0b6c71fddda6fc52fea853c96bb0109bfab Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 11 Nov 2024 13:56:20 -0800
Subject: [PATCH 09/15] add license file and use noarch generic now

---
 recipes/finemap/LICENSE   | 13 +++++++++++++
 recipes/finemap/meta.yaml |  4 +++-
 2 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 recipes/finemap/LICENSE

diff --git a/recipes/finemap/LICENSE b/recipes/finemap/LICENSE
new file mode 100644
index 0000000000000..d4687c556eba8
--- /dev/null
+++ b/recipes/finemap/LICENSE
@@ -0,0 +1,13 @@
+FINEMAP, (c) 2015-2020, The University of Helsinki (the "Software")
+
+The Software remains the property of the University of Helsinki ("the University").
+
+The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software.
+
+The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software.
+
+No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the Software, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions.
+
+You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received.
+
+The software uses unchanged open source components. The developers of these open source projects are hereby gratefully acknowledged. Source code of open source projects together with license information can be found below.
diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 0a8756c5dd17c..de1c17db6b65c 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -15,11 +15,12 @@ build:
   number: 0
   # skip broken osx for now
   skip: True # [not linux64]
+  noarch: generic
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
   script:
     - mkdir -p ${PREFIX}/bin
-    - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux]
+    - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux64]
     - install -m 755 finemap_v{{ version }}_MacOSX ${PREFIX}/bin/finemap # [osx]
 
 test:
@@ -29,6 +30,7 @@ test:
 about:
   home: http://www.christianbenner.com
   license: Other
+  license_url: http://www.christianbenner.com/license_finemap_v1.4.html
   license_file: LICENSE
   summary: >
     Program for identifying causal SNPs and their effect sizes and heritability contributions

From f1c75d62f4302283aecfa8840df885a956349d16 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 11 Nov 2024 15:19:40 -0800
Subject: [PATCH 10/15] completely give up on osx

The OSX binary will not work. It needs to be relinked so that the shared library paths point to the conda versions. But relinking doesn't work because the binary was not built with the -headerpad_max_install_names option
---
 recipes/finemap/meta.yaml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index de1c17db6b65c..7f152deb15a8f 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -6,22 +6,19 @@ package:
   version: {{ version }}
 
 source:
-  - url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz # [linux64]
-    sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 # [linux64]
-  - url: http://www.christianbenner.com/finemap_v{{ version }}_MacOSX.tgz # [osx]
-    sha256: e2967e5586347a8ac5cbcddf3c0e41bf8d3e7793875f78b509d07903d17a415b # [osx]
+  - url: http://www.christianbenner.com/finemap_v{{ version }}_x86_64.tgz
+    sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9
 
 build:
   number: 0
-  # skip broken osx for now
+  # skip osx since binary cannot be relinked b/c it was built without the -headerpad_max_install_names option
   skip: True # [not linux64]
   noarch: generic
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
   script:
     - mkdir -p ${PREFIX}/bin
-    - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap # [linux64]
-    - install -m 755 finemap_v{{ version }}_MacOSX ${PREFIX}/bin/finemap # [osx]
+    - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap
 
 test:
   commands:
@@ -29,7 +26,7 @@ test:
 
 about:
   home: http://www.christianbenner.com
-  license: Other
+  license: Custom Academic
   license_url: http://www.christianbenner.com/license_finemap_v1.4.html
   license_file: LICENSE
   summary: >

From 1696b5846f01b57bcd47c64a529def9d8fc94ef8 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 11 Nov 2024 15:25:48 -0800
Subject: [PATCH 11/15] remove noarch generic

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 recipes/finemap/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 7f152deb15a8f..fca8a9d65a288 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -13,7 +13,6 @@ build:
   number: 0
   # skip osx since binary cannot be relinked b/c it was built without the -headerpad_max_install_names option
   skip: True # [not linux64]
-  noarch: generic
   run_exports:
     - {{ pin_subpackage('finemap', max_pin="x") }}
   script:

From 83fc1dca54059e6a09712a4f7248d20325007483 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 11 Nov 2024 15:44:20 -0800
Subject: [PATCH 12/15] skip noarch generic lint

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

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index fca8a9d65a288..c397d3e8a2e0a 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -32,5 +32,7 @@ about:
     Program for identifying causal SNPs and their effect sizes and heritability contributions
 
 extra:
+  skip-lints:
+    - should_be_noarch_generic
   recipe-maintainers:
     - danielnachun

From acc89b49715599f82b5cf96b69d07ead56900a4a Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 13 Nov 2024 21:23:17 +0000
Subject: [PATCH 13/15] add required dependencies, use LICENSE from source, and
 use example data for tests

---
 recipes/finemap/LICENSE   | 13 -------------
 recipes/finemap/meta.yaml | 17 +++++++++++++++++
 2 files changed, 17 insertions(+), 13 deletions(-)
 delete mode 100644 recipes/finemap/LICENSE

diff --git a/recipes/finemap/LICENSE b/recipes/finemap/LICENSE
deleted file mode 100644
index d4687c556eba8..0000000000000
--- a/recipes/finemap/LICENSE
+++ /dev/null
@@ -1,13 +0,0 @@
-FINEMAP, (c) 2015-2020, The University of Helsinki (the "Software")
-
-The Software remains the property of the University of Helsinki ("the University").
-
-The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software.
-
-The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software.
-
-No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the Software, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions.
-
-You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received.
-
-The software uses unchanged open source components. The developers of these open source projects are hereby gratefully acknowledged. Source code of open source projects together with license information can be found below.
diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index c397d3e8a2e0a..832680d4aabf9 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -19,14 +19,30 @@ build:
     - mkdir -p ${PREFIX}/bin
     - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap
 
+requirements:
+  build:
+    - {{ stdlib("c") }}
+    - libgomp
+    - libgcc
+  run:
+    - {{ stdlib("c") }}
+    - libgomp
+    - libgcc
+
 test:
+  source_files:
+    - example
   commands:
     - finemap --help
+    - finemap --sss --in-files example/data
+    - finemap --cond --in-files example/data
+    - finemap --config --in-files example/data --rsids rs30,rs11
 
 about:
   home: http://www.christianbenner.com
   license: Custom Academic
   license_url: http://www.christianbenner.com/license_finemap_v1.4.html
+  # use LICENSE file in downloaded source
   license_file: LICENSE
   summary: >
     Program for identifying causal SNPs and their effect sizes and heritability contributions
@@ -35,4 +51,5 @@ extra:
   skip-lints:
     - should_be_noarch_generic
   recipe-maintainers:
+    - aryarm
     - danielnachun

From 41777dd07b7c6e38d17789de3802ae2d98423f63 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 13 Nov 2024 13:44:02 -0800
Subject: [PATCH 14/15] skip more lint checks

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

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 832680d4aabf9..4591aaec6d4a1 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -49,7 +49,9 @@ about:
 
 extra:
   skip-lints:
+    - should_use_compilers
     - should_be_noarch_generic
+    - version_constraints_missing_whitespace
   recipe-maintainers:
     - aryarm
     - danielnachun

From e610d615dcb9d6f1fa2c15c7840264b7ebf9b345 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Wed, 20 Nov 2024 10:29:40 -0800
Subject: [PATCH 15/15] move build requirements to host and whitelist

---
 recipes/finemap/meta.yaml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml
index 4591aaec6d4a1..10b7b977ddad4 100644
--- a/recipes/finemap/meta.yaml
+++ b/recipes/finemap/meta.yaml
@@ -18,9 +18,17 @@ build:
   script:
     - mkdir -p ${PREFIX}/bin
     - install -m 755 finemap_v{{ version }}_x86_64 ${PREFIX}/bin/finemap
+  missing_dso_whitelist:
+    - /lib64/libdl.so.2
+    - /lib64/libm.so.6
+    - $RPATH/libgomp.so.1
+    - /lib64/libgcc_s.so.1
+    - /lib64/libpthread.so.0
+    - /lib64/libc.so.6
+    - /lib64/ld-linux-x86-64.so.2
 
 requirements:
-  build:
+  host:
     - {{ stdlib("c") }}
     - libgomp
     - libgcc