From f5551c79d68910b5c97dadfc18eb4cfa605ed90d Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 08:14:49 +0000
Subject: [PATCH 1/3] Update genotyphi to 2.1

---
 recipes/genotyphi/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/genotyphi/meta.yaml b/recipes/genotyphi/meta.yaml
index 010e90af15eb0..e6fa08eb603ee 100644
--- a/recipes/genotyphi/meta.yaml
+++ b/recipes/genotyphi/meta.yaml
@@ -1,6 +1,6 @@
 {% set name="genotyphi" %}
-{% set version = "2.0" %}
-{% set sha256 = "ad1144fd94de00a3ece6abff08ae0d457760292747b87ddf3b64b2e5c83314ce" %}
+{% set version = "2.1" %}
+{% set sha256 = "bbb44b440b5fcfd792f633d7428e077a25b15a390d96af99748b178c8fa8c5b0" %}
 
 package:
   name: {{ name }}
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin='x') }}
 

From 0222d463b11b2fd23516d42836f40968250f7239 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Mon, 30 Sep 2024 10:40:18 -0500
Subject: [PATCH 2/3] clean up recipe

---
 recipes/genotyphi/build.sh  | 4 ++--
 recipes/genotyphi/meta.yaml | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/recipes/genotyphi/build.sh b/recipes/genotyphi/build.sh
index 3d0a5d709d8f4..02cad3b5754b6 100644
--- a/recipes/genotyphi/build.sh
+++ b/recipes/genotyphi/build.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 
 mkdir -p $PREFIX/bin
-cp genotyphi.py $PREFIX/bin/genotyphi.py
-ln $PREFIX/bin/genotyphi.py $PREFIX/bin/genotyphi
+cp mappingbased/genotyphi.py $PREFIX/bin/genotyphi.py
+ln -sf $PREFIX/bin/genotyphi.py $PREFIX/bin/genotyphi
 chmod +x $PREFIX/bin/genotyphi.py $PREFIX/bin/genotyphi
 
 # Add script for Mykrobe based analysis
diff --git a/recipes/genotyphi/meta.yaml b/recipes/genotyphi/meta.yaml
index e6fa08eb603ee..ab9dddcdb3bcb 100644
--- a/recipes/genotyphi/meta.yaml
+++ b/recipes/genotyphi/meta.yaml
@@ -33,6 +33,8 @@ test:
 
 about:
   home: https://github.com/typhoidgenomics/genotyphi
-  license: GPL3
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
   summary: Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
+  dev_url: https://github.com/typhoidgenomics/genotyphi

From 88c41d7ece704bc2a834bb9b1edd61a67ce09377 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Mon, 30 Sep 2024 11:09:22 -0500
Subject: [PATCH 3/3] clean up recipe

---
 recipes/genotyphi/build.sh  | 2 +-
 recipes/genotyphi/meta.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/genotyphi/build.sh b/recipes/genotyphi/build.sh
index 02cad3b5754b6..e0c809d30f2da 100644
--- a/recipes/genotyphi/build.sh
+++ b/recipes/genotyphi/build.sh
@@ -2,7 +2,7 @@
 
 mkdir -p $PREFIX/bin
 cp mappingbased/genotyphi.py $PREFIX/bin/genotyphi.py
-ln -sf $PREFIX/bin/genotyphi.py $PREFIX/bin/genotyphi
+ln $PREFIX/bin/genotyphi.py $PREFIX/bin/genotyphi
 chmod +x $PREFIX/bin/genotyphi.py $PREFIX/bin/genotyphi
 
 # Add script for Mykrobe based analysis
diff --git a/recipes/genotyphi/meta.yaml b/recipes/genotyphi/meta.yaml
index ab9dddcdb3bcb..0963798dfb8ae 100644
--- a/recipes/genotyphi/meta.yaml
+++ b/recipes/genotyphi/meta.yaml
@@ -20,7 +20,7 @@ requirements:
   host:
     - wget
   run:
-    - python <3
+    - python
     - samtools >=1.1
     - bcftools >=1.1
     - pandas