From 9bd42ce857658fb5ea4dd68855273a11f12e440b Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>
Date: Mon, 27 May 2024 17:28:02 +0200
Subject: [PATCH] Compatibility version bump of dependencies

- some old dependencies don't work anymore
- ngshmmalign, bwa_QA, initial_vicuna_msa, msa, testbench
  depency mafft: 7.305->7.526
- while we're at it, version bump smallgenomeutilities 0.4.1
---
 workflow/envs/bwa_QA.yaml               | 2 +-
 workflow/envs/hmm_align.yaml            | 2 +-
 workflow/envs/initial_vicuna_msa.yaml   | 4 ++--
 workflow/envs/msa.yaml                  | 2 +-
 workflow/envs/smallgenomeutilities.yaml | 2 +-
 workflow/envs/testbench.yaml            | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/workflow/envs/bwa_QA.yaml b/workflow/envs/bwa_QA.yaml
index b5e316d4..1167f450 100644
--- a/workflow/envs/bwa_QA.yaml
+++ b/workflow/envs/bwa_QA.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
 dependencies:
   - bwa=0.7.17
-  - mafft=7.458
+  - mafft=7.526
diff --git a/workflow/envs/hmm_align.yaml b/workflow/envs/hmm_align.yaml
index 923fee94..675a7411 100644
--- a/workflow/envs/hmm_align.yaml
+++ b/workflow/envs/hmm_align.yaml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - mafft=7.305
+  - mafft=7.526
   - ngshmmalign=0.1.1
diff --git a/workflow/envs/initial_vicuna_msa.yaml b/workflow/envs/initial_vicuna_msa.yaml
index d0f43042..6e180778 100644
--- a/workflow/envs/initial_vicuna_msa.yaml
+++ b/workflow/envs/initial_vicuna_msa.yaml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - mafft=7.458
-  - smallgenomeutilities=0.3.1
+  - mafft=7.526
+  - smallgenomeutilities=0.4.1
diff --git a/workflow/envs/msa.yaml b/workflow/envs/msa.yaml
index d90ff454..96a5ae3b 100644
--- a/workflow/envs/msa.yaml
+++ b/workflow/envs/msa.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - mafft=7.458
+  - mafft=7.526
diff --git a/workflow/envs/smallgenomeutilities.yaml b/workflow/envs/smallgenomeutilities.yaml
index 9fc4844a..d2cf70c9 100644
--- a/workflow/envs/smallgenomeutilities.yaml
+++ b/workflow/envs/smallgenomeutilities.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - smallgenomeutilities=0.3.9
+  - smallgenomeutilities=0.4.1
diff --git a/workflow/envs/testbench.yaml b/workflow/envs/testbench.yaml
index e967d9a4..cf7fe989 100644
--- a/workflow/envs/testbench.yaml
+++ b/workflow/envs/testbench.yaml
@@ -7,4 +7,4 @@ dependencies:
   - sh
   - biopython
   - pandas
-  - mafft=7.305
+  - mafft=7.526