From 74e6bd28126461d80a0552c315fa43040b39fb4e Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 13:10:40 +0000 Subject: [PATCH 1/8] Update artic to 1.5.1 --- recipes/artic/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 59642e631a4cb..cbd9c5770192c 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -1,6 +1,6 @@ {% set name = "artic" %} -{% set version = "1.2.4" %} -{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %} +{% set version = "1.5.1" %} +{% set sha256 = "f0917dac3707a664f5447d9bf5a2358a73def64ed6e0e96859cb5e02fefc8791" %} package: name: {{ name|lower }} @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage('artic', max_pin='x.x') }} From 387ae50082b33a42dba1291733c8679fa141f201 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 14:12:39 +0000 Subject: [PATCH 2/8] Update artic to 1.5.1 --- recipes/artic/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index cbd9c5770192c..b081095c70b18 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -1,6 +1,6 @@ {% set name = "artic" %} {% set version = "1.5.1" %} -{% set sha256 = "f0917dac3707a664f5447d9bf5a2358a73def64ed6e0e96859cb5e02fefc8791" %} +{% set sha256 = "6bbd5f07f1417ff046bdc17c57cf55871027738e082121e24c5b22593351d27b" %} package: name: {{ name|lower }} From a87a738ba50c1fe13d06be5c1375f83164f1eb4b Mon Sep 17 00:00:00 2001 From: Sam W Date: Wed, 13 Nov 2024 14:54:18 +0000 Subject: [PATCH 3/8] Fix dependencies --- recipes/artic/meta.yaml | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index b081095c70b18..845efa3242d63 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -28,37 +28,32 @@ build: - artic_fasta_header=artic.fasta_header:main - artic_mask=artic.mask:main - artic_get_stats=artic.artic_mqc:main + - artic_get_models=artic.get_models:main requirements: host: - python >=3 - pip run: - - python - - artic-porechop >=0.3.2pre - - artic-tools - - longshot + - python==3.9 - bcftools - biopython - bwa + - clair3 - clint - htslib - - medaka >=1.10.0 - - minimap2 >=2.26 + - minimap2 - multiqc - - muscle =3.8 - - nanopolish >=0.14.0 + - muscle<5.1 - pandas - pip - pysam - pytest - - pyvcf - - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE + - cyvcf2 + - pyfaidx=0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE - requests - samtools - tqdm - - keras-preprocessing >=1.1.2 - test: commands: @@ -74,6 +69,7 @@ test: - artic_fasta_header -h - artic_mask -h - artic_get_stats -h + - artic_get_models -h about: home: https://github.com/artic-network/fieldbioinformatics From 59bd96d429f3ad612bd008c0e4a03dff9b68741f Mon Sep 17 00:00:00 2001 From: Sam W Date: Wed, 13 Nov 2024 14:58:19 +0000 Subject: [PATCH 4/8] Update meta.yaml --- recipes/artic/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 845efa3242d63..2934000e58d32 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -35,7 +35,7 @@ requirements: - python >=3 - pip run: - - python==3.9 + - python ==3.9 - bcftools - biopython - bwa @@ -44,13 +44,13 @@ requirements: - htslib - minimap2 - multiqc - - muscle<5.1 + - muscle <5.1 - pandas - pip - pysam - pytest - cyvcf2 - - pyfaidx=0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE + - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE - requests - samtools - tqdm From 10066f45e1d504dd551451407e18b80bef50ecf5 Mon Sep 17 00:00:00 2001 From: Sam W Date: Wed, 13 Nov 2024 15:15:03 +0000 Subject: [PATCH 5/8] Update meta.yaml --- recipes/artic/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 2934000e58d32..5d1f7e39d29c4 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -34,6 +34,7 @@ requirements: host: - python >=3 - pip + - setuptools run: - python ==3.9 - bcftools From ddc82d118ed5be0ca2ac570fd5cb170bf71f901c Mon Sep 17 00:00:00 2001 From: Sam W Date: Wed, 13 Nov 2024 15:25:21 +0000 Subject: [PATCH 6/8] Update meta.yaml --- recipes/artic/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 5d1f7e39d29c4..c3e121df202d1 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -32,7 +32,7 @@ build: requirements: host: - - python >=3 + - python ==3.9 - pip - setuptools run: From 139fa5547da308f581239a7ce9f77b76343665cb Mon Sep 17 00:00:00 2001 From: Sam W Date: Wed, 13 Nov 2024 15:47:02 +0000 Subject: [PATCH 7/8] Update meta.yaml --- recipes/artic/meta.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index c3e121df202d1..d2a37e4ab6280 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -18,16 +18,13 @@ build: entry_points: - artic=artic.pipeline:main - align_trim=artic.align_trim:main - - align_trim_n=artic.align_trim_n:main - margin_cons=artic.margin_cons:main - - margin_cons_medaka=artic.margin_cons_medaka:main - vcfextract=artic.vcfextract:main - artic_vcf_merge=artic.vcf_merge:main - artic_vcf_filter=artic.vcf_filter:main - artic_make_depth_mask=artic.make_depth_mask:main - artic_fasta_header=artic.fasta_header:main - artic_mask=artic.mask:main - - artic_get_stats=artic.artic_mqc:main - artic_get_models=artic.get_models:main requirements: From ea1659af2c323631482e093754482ff6928ec0c7 Mon Sep 17 00:00:00 2001 From: Sam W Date: Wed, 13 Nov 2024 15:47:30 +0000 Subject: [PATCH 8/8] Update meta.yaml --- recipes/artic/meta.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index d2a37e4ab6280..6238f8b96b643 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -57,16 +57,13 @@ test: commands: - artic -h - align_trim -h - - align_trim_n -h - margin_cons -h - - margin_cons_medaka -h - vcfextract -h - artic_vcf_merge -h - artic_vcf_filter -h - artic_make_depth_mask -h - artic_fasta_header -h - artic_mask -h - - artic_get_stats -h - artic_get_models -h about: