From 098178abb1e7459a7e5eea7e496c6e3d50535072 Mon Sep 17 00:00:00 2001
From: Adam Diehl <adadiehl@umich.edu>
Date: Tue, 10 Dec 2024 15:07:23 -0500
Subject: [PATCH 1/4] Add recipe for GPatch

---
 recipes/gpatch/meta.yaml | 41 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 recipes/gpatch/meta.yaml

diff --git a/recipes/gpatch/meta.yaml b/recipes/gpatch/meta.yaml
new file mode 100644
index 0000000000000..5b05f0295a12a
--- /dev/null
+++ b/recipes/gpatch/meta.yaml
@@ -0,0 +1,41 @@
+{% set name = "GPatch" %}
+{% set version = "0.3.0" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: 512eff3702a2cbfb01b03a8b195b44562f74cd6203b769dd08095f6bc3741b8f
+
+build:
+  number: 0
+  entry_points:
+    - GPatch = GPatch.GPatch:main
+  script: "{{ PYTHON }} -m pip install . -vv"
+  noarch: python
+  run_exports:
+    - {{ pin_subpackage('gpatch', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.7,<3.13
+    - pip
+  run:
+    - python >=3.7,<3.13
+    - Bio >=1.84
+    - pysam >=0.22.1
+
+test:
+  imports:
+    - GPatch
+  commands:
+    - GPatch --help
+
+about:
+  home: "https://github.com/adadiehl/GPatch.git"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference."

From 81f152035ca93d0b7bb2ec7a8df4c1b2e6c8cfaf Mon Sep 17 00:00:00 2001
From: Adam Diehl <adadiehl@umich.edu>
Date: Tue, 10 Dec 2024 15:22:36 -0500
Subject: [PATCH 2/4] Fix dependencies

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

diff --git a/recipes/gpatch/meta.yaml b/recipes/gpatch/meta.yaml
index 5b05f0295a12a..8ab32e56396e2 100644
--- a/recipes/gpatch/meta.yaml
+++ b/recipes/gpatch/meta.yaml
@@ -24,7 +24,7 @@ requirements:
     - pip
   run:
     - python >=3.7,<3.13
-    - Bio >=1.84
+    - biopython >=1.84
     - pysam >=0.22.1
 
 test:

From 2f3fe80739714b1697a68bf557b747b2fdfe31cb Mon Sep 17 00:00:00 2001
From: Adam Diehl <adadiehl@umich.edu>
Date: Tue, 10 Dec 2024 16:03:14 -0500
Subject: [PATCH 3/4] Should fix module not found error

---
 recipes/gpatch/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/gpatch/meta.yaml b/recipes/gpatch/meta.yaml
index 8ab32e56396e2..fc604151ad068 100644
--- a/recipes/gpatch/meta.yaml
+++ b/recipes/gpatch/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "GPatch" %}
-{% set version = "0.3.0" %}
+{% set version = "0.3.4" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 512eff3702a2cbfb01b03a8b195b44562f74cd6203b769dd08095f6bc3741b8f
+  sha256: 243b63181500dabdc4934cb2433e13448f710fff2211e28af46ca365ca418c5a
 
 build:
   number: 0

From 64be706a257633addd8329e11825b827dfdb6264 Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Wed, 11 Dec 2024 08:08:34 +0200
Subject: [PATCH 4/4] fix the max_pin value

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

diff --git a/recipes/gpatch/meta.yaml b/recipes/gpatch/meta.yaml
index fc604151ad068..178e0ca32d63f 100644
--- a/recipes/gpatch/meta.yaml
+++ b/recipes/gpatch/meta.yaml
@@ -16,7 +16,7 @@ build:
   script: "{{ PYTHON }} -m pip install . -vv"
   noarch: python
   run_exports:
-    - {{ pin_subpackage('gpatch', max_pin="x") }}
+    - {{ pin_subpackage('gpatch', max_pin="x.x") }}
 
 requirements:
   host: