From 4f6c699642143cd0de922b52a00d23a9255ee441 Mon Sep 17 00:00:00 2001
From: "N. Tessa Pierce" <ntpierce@gmail.com>
Date: Mon, 16 May 2022 15:00:30 -0700
Subject: [PATCH] mamba env for installations; use compare --avg-containment
 --ani

---
 compare_matrices.py |  2 +-
 environment.yml     | 14 ++++++++++++++
 2 files changed, 15 insertions(+), 1 deletion(-)
 create mode 100644 environment.yml

diff --git a/compare_matrices.py b/compare_matrices.py
index 85f8095..3cac7eb 100644
--- a/compare_matrices.py
+++ b/compare_matrices.py
@@ -84,7 +84,7 @@
 subprocess.call(sketch_command, shell=True)
 # Then run sourmash compare with ANI
 save_prefix = 'sourmash_compare_ANI'
-compare_ANI_command = f"sourmash compare -k 21 --ani -o {save_prefix}.cmp "
+compare_ANI_command = f"sourmash compare -k 21 --ani --avg-containment -o {save_prefix}.cmp "
 for _, gpath in genome_list:
     sig_path = os.path.join(sketch_dir, gpath.split('/')[-1]) + '.sig'
     compare_ANI_command += sig_path + ' '
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..f8de887
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,14 @@
+name: phylo-ani
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - sourmash=4.4
+  - biopython
+  - mmh3
+  # temporary: install sourmash 'latest' branch to get `--avg-containment`
+  - rust
+  - pip
+  - pip:
+    - git+https://github.com/sourmash-bio/sourmash@latest