From c9a19dfafe0437a04beabfacce1b5a8770f0f9d7 Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Wed, 10 Jul 2024 16:45:33 -0700
Subject: [PATCH] Fix fluviewer installation in consistency check workflow

---
 .github/environments/fluviewer-bccdc-phl.yml  | 18 +++++++++++++++++
 .github/environments/fluviewer-kkuchinski.yml | 20 +++++++++++++++++++
 .../scripts/install_fluviewer_bccdc-phl.sh    |  2 +-
 .../scripts/install_fluviewer_kkuchinski.sh   |  6 +-----
 4 files changed, 40 insertions(+), 6 deletions(-)
 create mode 100644 .github/environments/fluviewer-bccdc-phl.yml
 create mode 100644 .github/environments/fluviewer-kkuchinski.yml

diff --git a/.github/environments/fluviewer-bccdc-phl.yml b/.github/environments/fluviewer-bccdc-phl.yml
new file mode 100644
index 0000000..b8d3ee1
--- /dev/null
+++ b/.github/environments/fluviewer-bccdc-phl.yml
@@ -0,0 +1,18 @@
+name: fluviewer-bccdc-phl
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - bbmap=39.01
+  - bcftools=1.17
+  - blast=2.14.1
+  - bwa=0.7.17
+  - samtools=1.17
+  - spades=4.0.0
+  - clustalw=2.1
+  - freebayes=1.3.6
+  - python=3
+  - pip
+  - pandas=2.0.3
+  - seaborn=0.12.2
diff --git a/.github/environments/fluviewer-kkuchinski.yml b/.github/environments/fluviewer-kkuchinski.yml
new file mode 100644
index 0000000..26c9a83
--- /dev/null
+++ b/.github/environments/fluviewer-kkuchinski.yml
@@ -0,0 +1,20 @@
+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
+  - pip
+  - pandas=2.0.3
+  - seaborn=0.12.2
+  - pip:
+    - FluViewer==0.1.11
diff --git a/.github/scripts/install_fluviewer_bccdc-phl.sh b/.github/scripts/install_fluviewer_bccdc-phl.sh
index 89834c7..8deb97c 100755
--- a/.github/scripts/install_fluviewer_bccdc-phl.sh
+++ b/.github/scripts/install_fluviewer_bccdc-phl.sh
@@ -4,7 +4,7 @@ source ${HOME}/.bashrc
  
 eval "$(conda shell.bash hook)"
 
-conda env create -f environment.yaml -n fluviewer-bccdc-phl
+conda env create -f .github/environments/fluviewer-bccdc-phl.yml -n fluviewer-bccdc-phl
 
 conda activate fluviewer-bccdc-phl
 
diff --git a/.github/scripts/install_fluviewer_kkuchinski.sh b/.github/scripts/install_fluviewer_kkuchinski.sh
index f7b2bfc..0dc7c9d 100755
--- a/.github/scripts/install_fluviewer_kkuchinski.sh
+++ b/.github/scripts/install_fluviewer_kkuchinski.sh
@@ -6,8 +6,4 @@ 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.yml -n fluviewer-kkuchinski