From 79dbad800ce3412f1265c7030815b1ae008f8e88 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Mar 2024 13:27:34 -0400
Subject: [PATCH] Update busco to 5.7.0 (#46490)

* Update busco to 5.7.0

* Constrain biopython; add patch

---------

Co-authored-by: Matthew Berkeley <42berkeley@cua.edu>
---
 .../busco/0001-Set-conda-distribution.patch   | 23 +++++++++++++++++++
 recipes/busco/meta.yaml                       |  8 +++----
 2 files changed, 27 insertions(+), 4 deletions(-)
 create mode 100644 recipes/busco/0001-Set-conda-distribution.patch

diff --git a/recipes/busco/0001-Set-conda-distribution.patch b/recipes/busco/0001-Set-conda-distribution.patch
new file mode 100644
index 0000000000000..b8a0ac5f2531e
--- /dev/null
+++ b/recipes/busco/0001-Set-conda-distribution.patch
@@ -0,0 +1,23 @@
+--- a/src/busco/run_BUSCO.py
++++ b/src/busco/run_BUSCO.py
+@@ -121,18 +121,12 @@ class BuscoMaster:
+             logger.debug("File upload failed. Status code: {}".format(response.status))
+ 
+     def get_dist_info(self):
+-        if (  # todo: fix
+-            "conda" in __file__
+-            and os.environ("CONDA_DEFAULT_ENV")
+-            and os.environ("CONDA_PREFIX")
+-        ):
+-            self.run_data["distribution"] = "conda"
+-        elif os.path.exists("/.dockerenv"):
++        if os.path.exists("/.dockerenv"):
+             self.run_data["distribution"] = "docker"
+         elif os.path.exists("/.singularity.d"):
+             self.run_data["distribution"] = "singularity"
+         else:
+-            self.run_data["distribution"] = "manual"
++            self.run_data["distribution"] = "conda"
+ 
+     def get_download_url(self):
+         if self.config.getboolean("busco_run", "offline"):
diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml
index 515c990c241e1..a6261567bb48f 100644
--- a/recipes/busco/meta.yaml
+++ b/recipes/busco/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "busco" %}
-{% set version = "5.6.1" %}
-{% set sha256 = "1129d8dd1779455b77c47a926650e1974aaca58eeb9e6b3b6e4a706154ab2da8" %}
+{% set version = "5.7.0" %}
+{% set sha256 = "dbd9e07a5fb42583bd6ddbbfe06c420d5317a6f3698e6f4be0f53baa6c3ccc5e" %}
 
 package:
   name: busco
@@ -26,7 +26,7 @@ requirements:
     - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
     - hmmer >=3.1b2 # sepp needs this version
     - augustus >=3.3
-    - biopython
+    - biopython >=1.79
     - prodigal
     - sepp >=4.3.10
     - dendropy <4.6.0  # necessary temporarily until SEPP updates their codebase or recipe
@@ -41,7 +41,7 @@ requirements:
     - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
     - hmmer >=3.1b2 # sepp needs this version
     - augustus >=3.3
-    - biopython
+    - biopython >=1.79
     - r-base
     - r-ggplot2 >=2.2.1
     - prodigal