From e2bb64ca1cb8800535027ce33bda56369d56e94b Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Thu, 6 Aug 2026 12:11:01 +0200 Subject: [PATCH 1/4] GSL fixed * Reentered module which would not work on OSX due to libgsl issues. Now assumed to be fixed on bioconda * Changed assembler to skesa on assembler dependent modules --- src/mmaseq/config/species_configs/test.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/mmaseq/config/species_configs/test.yaml b/src/mmaseq/config/species_configs/test.yaml index f8bea16..fa790b9 100644 --- a/src/mmaseq/config/species_configs/test.yaml +++ b/src/mmaseq/config/species_configs/test.yaml @@ -78,9 +78,9 @@ lrefinder: database : elmDB reads: True -# kleborate: # MacOS gsl=2.5 -# options: --preset escherichia -# assembler: spades +kleborate: # MacOS gsl=2.5 + options: --preset escherichia + assembler: skesa # meningotype: # MacOS # assembler: spades @@ -88,9 +88,8 @@ lrefinder: spatyper: assembler: spades -# seqsero2: # MacOS -# assembler: spades - +seqsero2: # MacOS + assembler: skesa sistr: assembler: spades From 0d03751a0e85f6243cf7f15f09874fced79a4922 Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Thu, 6 Aug 2026 12:18:12 +0200 Subject: [PATCH 2/4] Remove version constraint for seqsero2 dependency Due to resolvement issues, constraints have been removed --- src/mmaseq/workflow/envs/seqsero2.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mmaseq/workflow/envs/seqsero2.yaml b/src/mmaseq/workflow/envs/seqsero2.yaml index c81c0a8..a7c5242 100644 --- a/src/mmaseq/workflow/envs/seqsero2.yaml +++ b/src/mmaseq/workflow/envs/seqsero2.yaml @@ -1,3 +1,3 @@ name: seqsero2 dependencies: - - bioconda::seqsero2=1.3.1 + - bioconda::seqsero2 From 483a2c01d71469b90461aa2ec6998b727560e930 Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Thu, 6 Aug 2026 14:05:40 +0200 Subject: [PATCH 3/4] Disable kleborate settings in test.yaml Comment out kleborate configuration in test.yaml --- src/mmaseq/config/species_configs/test.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/mmaseq/config/species_configs/test.yaml b/src/mmaseq/config/species_configs/test.yaml index fa790b9..744a556 100644 --- a/src/mmaseq/config/species_configs/test.yaml +++ b/src/mmaseq/config/species_configs/test.yaml @@ -78,9 +78,9 @@ lrefinder: database : elmDB reads: True -kleborate: # MacOS gsl=2.5 - options: --preset escherichia - assembler: skesa +# kleborate: # MacOS gsl=2.5 +# options: --preset escherichia +# assembler: skesa # meningotype: # MacOS # assembler: spades From f1484ec02b965b2a86a522142b076ced8addaa0a Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Sun, 9 Aug 2026 09:55:30 +0200 Subject: [PATCH 4/4] Seqsero removed and testing kleborate on macOS --- src/mmaseq/config/species_configs/test.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/mmaseq/config/species_configs/test.yaml b/src/mmaseq/config/species_configs/test.yaml index 744a556..6f69ad5 100644 --- a/src/mmaseq/config/species_configs/test.yaml +++ b/src/mmaseq/config/species_configs/test.yaml @@ -78,9 +78,9 @@ lrefinder: database : elmDB reads: True -# kleborate: # MacOS gsl=2.5 -# options: --preset escherichia -# assembler: skesa +kleborate: # MacOS gsl=2.5 + options: --preset escherichia + assembler: skesa # meningotype: # MacOS # assembler: spades @@ -88,8 +88,8 @@ lrefinder: spatyper: assembler: spades -seqsero2: # MacOS - assembler: skesa +# seqsero2: # MacOS +# assembler: skesa sistr: assembler: spades