pin mamba in aviary env

fixes libmamba error
AroneyS · Nov 29, 2024 · 4e21d4e · 4e21d4e
1 parent a659938
commit 4e21d4e
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/binchicken/workflow/coassemble.smk b/binchicken/workflow/coassemble.smk
@@ -834,7 +834,6 @@ rule aviary_assemble:
         "-n {threads} "
         "-t {threads} "
         "-m {resources.mem_gb} "
-        "--conda-frontend conda " # Mamba is causing errors: libmamba Non-conda folder exists at prefix
         "--skip-qc "
         "{resources.assembler} "
         "{params.dryrun} "
@@ -890,7 +889,6 @@ rule aviary_recover:
         "-n {params.threads} "
         "-t {params.threads} "
         "-m {resources.mem_gb} "
-        "--conda-frontend conda " # Mamba is causing errors: libmamba Non-conda folder exists at prefix
         "--skip-qc "
         "{params.snakemake_profile} "
         "{params.cluster_retries} "

diff --git a/binchicken/workflow/env/aviary.yml b/binchicken/workflow/env/aviary.yml
@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - aviary=0.10.*
+  - mamba=1.4.*