From 83a3f4a5a855887dedb7dc18afb3ac261c59bea4 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Sun, 24 Mar 2024 21:26:11 -0500 Subject: [PATCH 1/5] Update dram version --- recipes/dram/fix_setup.patch | 11 +++++++++++ recipes/dram/meta.yaml | 10 ++++++---- 2 files changed, 17 insertions(+), 4 deletions(-) create mode 100644 recipes/dram/fix_setup.patch diff --git a/recipes/dram/fix_setup.patch b/recipes/dram/fix_setup.patch new file mode 100644 index 0000000000000..0bc95bf5feddd --- /dev/null +++ b/recipes/dram/fix_setup.patch @@ -0,0 +1,11 @@ +--- scripts/DRAM-setup.py.old 2024-03-24 21:08:37.875167764 -0500 ++++ scripts/DRAM-setup.py 2024-03-24 21:16:33.729641778 -0500 +@@ -120,7 +120,7 @@ + set_db_locs_parser.add_argument('--vog_annotations_loc', default=None, + help='vog annotations file') # add loc to vog_annotations to match the rest + +- set_db_locs_parser.add_argument('--viral_loc', default=None, ++ set_db_locs_parser.add_argument('--viral_loc', default=None) + set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None, + help="The source for the CAMPER database files, this is a tar.gz file downloaded" + " from the release page https://github.com/WrightonLabCSU/CAMPER/releases") diff --git a/recipes/dram/meta.yaml b/recipes/dram/meta.yaml index 6c93600ad8052..886e73479c7fa 100644 --- a/recipes/dram/meta.yaml +++ b/recipes/dram/meta.yaml @@ -1,7 +1,7 @@ {% set name = "DRAM" %} {% set pypi_name = "DRAM-bio" %} -{% set version = "1.4.6" %} -{% set sha256 = "f014c55d7e75433bfc029dc20092df6eb9fb5a565dc60d6e7934d0261f36f945" %} +{% set version = "1.5.0" %} +{% set sha256 = "2d4a503fa806e33b580afb6d21879b2399178e48ba3b05ada882449fee571889" %} package: name: {{ name|lower }} @@ -12,13 +12,15 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" + patches: + - fix_setup.patch requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - python >=3.8 From 12cf690524b3a62bfc8ed9121d613e5a7d1cdf31 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Sun, 24 Mar 2024 21:26:48 -0500 Subject: [PATCH 2/5] Add github issue link --- recipes/dram/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/dram/meta.yaml b/recipes/dram/meta.yaml index 886e73479c7fa..5e2964f844cc6 100644 --- a/recipes/dram/meta.yaml +++ b/recipes/dram/meta.yaml @@ -16,6 +16,7 @@ build: noarch: python script: "{{ PYTHON }} -m pip install . -vv" patches: + # https://github.com/WrightonLabCSU/DRAM/issues/339 - fix_setup.patch requirements: From 7ec58e74b535b43df86d07fbea4eecec21e2bd3e Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Sun, 24 Mar 2024 21:28:45 -0500 Subject: [PATCH 3/5] Add run_exports --- recipes/dram/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/dram/meta.yaml b/recipes/dram/meta.yaml index 5e2964f844cc6..153b8fcb3d352 100644 --- a/recipes/dram/meta.yaml +++ b/recipes/dram/meta.yaml @@ -18,6 +18,8 @@ build: patches: # https://github.com/WrightonLabCSU/DRAM/issues/339 - fix_setup.patch + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: host: From 0e2814304c5a335ae891f6bf44ae0a875efc4d48 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Sun, 24 Mar 2024 21:50:34 -0500 Subject: [PATCH 4/5] Fix patches location --- recipes/dram/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/dram/meta.yaml b/recipes/dram/meta.yaml index 153b8fcb3d352..71f440a076c1b 100644 --- a/recipes/dram/meta.yaml +++ b/recipes/dram/meta.yaml @@ -10,14 +10,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ pypi_name }}/{{ pypi_name }}-{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + # https://github.com/WrightonLabCSU/DRAM/issues/339 + - fix_setup.patch build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" - patches: - # https://github.com/WrightonLabCSU/DRAM/issues/339 - - fix_setup.patch run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} From 12a8edeab93034c67b1fe6ce5f54ce3daae3c52b Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Sun, 24 Mar 2024 22:11:24 -0500 Subject: [PATCH 5/5] Fix patch --- recipes/dram/fix_setup.patch | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/recipes/dram/fix_setup.patch b/recipes/dram/fix_setup.patch index 0bc95bf5feddd..f8fb0fcc6f255 100644 --- a/recipes/dram/fix_setup.patch +++ b/recipes/dram/fix_setup.patch @@ -1,11 +1,14 @@ ---- scripts/DRAM-setup.py.old 2024-03-24 21:08:37.875167764 -0500 -+++ scripts/DRAM-setup.py 2024-03-24 21:16:33.729641778 -0500 -@@ -120,7 +120,7 @@ - set_db_locs_parser.add_argument('--vog_annotations_loc', default=None, +--- scripts/DRAM-setup.py.old 2024-03-24 22:09:07.980198244 -0500 ++++ scripts/DRAM-setup.py 2024-03-24 22:10:39.107097364 -0500 +@@ -121,10 +121,10 @@ help='vog annotations file') # add loc to vog_annotations to match the rest -- set_db_locs_parser.add_argument('--viral_loc', default=None, -+ set_db_locs_parser.add_argument('--viral_loc', default=None) + set_db_locs_parser.add_argument('--viral_loc', default=None, ++ help='mmseqs2 database file from ref seq viral gene collection') set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None, - help="The source for the CAMPER database files, this is a tar.gz file downloaded" - " from the release page https://github.com/WrightonLabCSU/CAMPER/releases") + help='The source for the CAMPER database files, this is a tar.gz file downloaded' + ' from the release page https://github.com/WrightonLabCSU/CAMPER/releases') +- help='mmseqs2 database file from ref seq viral gene collection') + set_db_locs_parser.add_argument('--peptidase_loc', default=None, + help='mmseqs2 database file from MEROPS database') + set_db_locs_parser.add_argument('--description_db_loc', default=None,