From d1c5c4087a7e4bf253ad5e451c2a84420248b52b Mon Sep 17 00:00:00 2001 From: AroneyS Date: Mon, 25 Nov 2024 08:10:46 +1000 Subject: [PATCH 1/3] bump aviary to v0.10.0 fixes vamb bins being ignored by dastool --- binchicken/workflow/env/aviary.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binchicken/workflow/env/aviary.yml b/binchicken/workflow/env/aviary.yml index cf4d23a4..68fece4e 100644 --- a/binchicken/workflow/env/aviary.yml +++ b/binchicken/workflow/env/aviary.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - aviary=0.9.* + - aviary=0.10.* From 6c664fc57028fc66cabed43a0b2ccd74f56d801c Mon Sep 17 00:00:00 2001 From: AroneyS Date: Tue, 26 Nov 2024 14:14:55 +1000 Subject: [PATCH 2/3] restrict to conda frontend mamba causing errors: libmamba Non-conda folder exists at prefix --- binchicken/workflow/coassemble.smk | 2 ++ 1 file changed, 2 insertions(+) diff --git a/binchicken/workflow/coassemble.smk b/binchicken/workflow/coassemble.smk index 99fcbb40..c29a2f42 100644 --- a/binchicken/workflow/coassemble.smk +++ b/binchicken/workflow/coassemble.smk @@ -834,6 +834,7 @@ 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} " @@ -889,6 +890,7 @@ 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} " From b6a9e6c83128f1c3ac1ac0d71d4548db14706f0d Mon Sep 17 00:00:00 2001 From: AroneyS Date: Fri, 29 Nov 2024 08:04:41 +1000 Subject: [PATCH 3/3] pin mamba in aviary env fixes libmamba error --- binchicken/workflow/coassemble.smk | 2 -- binchicken/workflow/env/aviary.yml | 1 + 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/binchicken/workflow/coassemble.smk b/binchicken/workflow/coassemble.smk index c29a2f42..99fcbb40 100644 --- 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 index 68fece4e..9be457de 100644 --- 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.*