From a7efe7d0539d48146e0255850091d71e9f23a859 Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Wed, 10 Jul 2024 19:55:46 -0700
Subject: [PATCH] Pin setuptools=69 (#39)

---
 .../environments/fluviewer-kkuchinski.yaml    | 21 +++++++++++++++++++
 .../scripts/install_fluviewer_kkuchinski.sh   |  8 +------
 environment.yaml                              |  1 +
 3 files changed, 23 insertions(+), 7 deletions(-)
 create mode 100644 .github/environments/fluviewer-kkuchinski.yaml

diff --git a/.github/environments/fluviewer-kkuchinski.yaml b/.github/environments/fluviewer-kkuchinski.yaml
new file mode 100644
index 0000000..d37e8c3
--- /dev/null
+++ b/.github/environments/fluviewer-kkuchinski.yaml
@@ -0,0 +1,21 @@
+name: fluviewer-kkuchinski
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - bbmap=39.01
+  - bcftools=1.17
+  - blast=2.14.1
+  - bwa=0.7.17
+  - samtools=1.17
+  - spades=3.15.3
+  - clustalw=2.1
+  - freebayes=1.3.6
+  - python=3
+  - setuptools=69
+  - pip
+  - pandas=2.0.3
+  - seaborn=0.12.2
+  - pip:
+    - FluViewer==0.1.11
diff --git a/.github/scripts/install_fluviewer_kkuchinski.sh b/.github/scripts/install_fluviewer_kkuchinski.sh
index f7b2bfc..aacee28 100755
--- a/.github/scripts/install_fluviewer_kkuchinski.sh
+++ b/.github/scripts/install_fluviewer_kkuchinski.sh
@@ -4,10 +4,4 @@ source ${HOME}/.bashrc
  
 eval "$(conda shell.bash hook)"
 
-fluviewer_version="0.1.11"
-
-conda env create -f environment.yaml -n fluviewer-kkuchinski
-
-conda activate fluviewer-kkuchinski
-
-pip install fluviewer==${fluviewer_version}
+conda env create -f .github/environments/fluviewer-kkuchinski.yaml
diff --git a/environment.yaml b/environment.yaml
index d0cba75..4823d8d 100644
--- a/environment.yaml
+++ b/environment.yaml
@@ -13,6 +13,7 @@ dependencies:
   - clustalw=2.1
   - freebayes=1.3.6
   - python=3
+  - setuptools=69
   - pip
   - pandas=2.0.3
   - seaborn=0.12.2