From cb93e7e5a18e1096285961802f754e16296652e6 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 13 Jun 2023 14:33:29 -0700 Subject: [PATCH 01/45] Add recipe for saccharis 2.0 dev18 build 1 to bioconda --- recipes/saccharis/LICENSE | 674 ++++++++++++++++++++++++++++++++++++ recipes/saccharis/icon.png | Bin 0 -> 40524 bytes recipes/saccharis/meta.yaml | 85 +++++ 3 files changed, 759 insertions(+) create mode 100644 recipes/saccharis/LICENSE create mode 100644 recipes/saccharis/icon.png create mode 100644 recipes/saccharis/meta.yaml diff --git a/recipes/saccharis/LICENSE b/recipes/saccharis/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/saccharis/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. 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https://github.com/AlexSCFraser/saccharis2.git + git_url: https://github.com/saccharis/SACCHARIS_2.git + git_depth: 1 # only grab most recent commit on branch + +build: + noarch: python +# number: {{ data.get('build') }} + number: 1 + script: {{ PYTHON }} setup.py install + preserve_egg_dir: True # added because the entry points below seem to be causing a build error + entry_points: + - saccharis = saccharis.CLI:cli_main + - saccharis.make_family_files = saccharis.utils.FamilyCategories:cli_main + - saccharis.add_family_category = saccharis.utils.FamilyCategories:cli_append_user_family + - saccharis.rename_user_file = saccharis.utils.UserFastaRename:cli_main + - saccharis.prune_seqs = saccharis.ExtractAndPruneCAZymes:cli_prune_seqs + - saccharis.screen_cazome = saccharis.ScreenUserFile:cli_cazome + - saccharis.show_family_categories = saccharis.utils.FamilyCategories:show_categories + - saccharis-gui = saccharis.gui.PipelineGUI:main + +requirements: + build: + - python + - setuptools + host: + - python + run: + - beautifulsoup4 >=4.11.1 + - biopython >=1.79 + - dbcan >=3.0.6, < 4 # [not win] + - diamond >=2.0.15 # [not win] + - fasttree >=2.1.11 # [not win] + - hmmer >=3.3 # [not win] + - lxml >=4.9.0 + - modeltest-ng >=0.1.7 # [not win] + - muscle >=3.8 # [not win] + - psutil + - python >=3.8 + - python-dotenv >=0.20.0 + - python-wget >=3.2 + - raxml >=8.2.12 # [not win] + - requests >=2.28.0 + - pyqt >=5,<6 + - pyqt5-sip >=12.11 +# - pip: +# - lxml >=4.9.0 +# - pyqt >=5,<6 +# - pyqt5-sip >=12.11 + +app: + entry: saccharis-gui + icon: icon.png + summary: "SACCHARIS Bioinformatics Pipeline" + + # output section does not work +#outputs: +# - name: saccharis2 +# files: +# - ../src/utils/*.py +# - ../src/*.py +# - ../src/config/*.json + +test: + commands: + - saccharis -v + - saccharis.make_family_files + - saccharis.show_family_categories + +about: + home: https://github.com/saccharis/SACCHARIS_2 + dev_url: https://github.com/saccharis/SACCHARIS_2 + description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences + license: GPL v3 + license_file: LICENSE + summary: A CAZyme discovery tool. From f6f773d79851f991f81406b62414adc9e32b74a3 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 14:30:01 -0700 Subject: [PATCH 02/45] updated to use git tag --- recipes/saccharis/meta.yaml | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 555954039e2ce..72c824b392c3f 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,21 +1,24 @@ #{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %} {% set name = "SACCHARIS" %} + {% set version = "2.0.0.dev18" %} + {% set build_no = 0 %} package: name: "{{ name|lower }}" # version: {{ data.get('version') }} - version: "2.0.0.dev18" + version: "{{ version }}" source: # path: ./.. # git_url: https://github.com/AlexSCFraser/saccharis2.git +# git_url: https://github.com/saccharis/SACCHARIS_2/tree/release.git git_url: https://github.com/saccharis/SACCHARIS_2.git - git_depth: 1 # only grab most recent commit on branch + git_tag: v{{ version }} build: noarch: python # number: {{ data.get('build') }} - number: 1 + number: {{ build_no }} script: {{ PYTHON }} setup.py install preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: @@ -33,7 +36,7 @@ requirements: - python - setuptools host: - - python + - python >=3.6 run: - beautifulsoup4 >=4.11.1 - biopython >=1.79 @@ -52,6 +55,7 @@ requirements: - requests >=2.28.0 - pyqt >=5,<6 - pyqt5-sip >=12.11 +# sort out pyqt5 install issues, sometimes pip seemed to install it with fewer errors? # - pip: # - lxml >=4.9.0 # - pyqt >=5,<6 @@ -62,16 +66,9 @@ app: icon: icon.png summary: "SACCHARIS Bioinformatics Pipeline" - # output section does not work -#outputs: -# - name: saccharis2 -# files: -# - ../src/utils/*.py -# - ../src/*.py -# - ../src/config/*.json - test: commands: + #future todo: pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests - saccharis -v - saccharis.make_family_files - saccharis.show_family_categories From d37cc1b441eaab0c495d1b88df88f6b64a02377f Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 16:41:15 -0700 Subject: [PATCH 03/45] updated to use a python package generated from setuptools build, with sha256 hash, and added --single-version-externally-managed --record=record.txt args to setup.py install as per bioconda test suite --- recipes/saccharis/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 72c824b392c3f..3b93099e55186 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -9,17 +9,18 @@ package: version: "{{ version }}" source: -# path: ./.. - # git_url: https://github.com/AlexSCFraser/saccharis2.git -# git_url: https://github.com/saccharis/SACCHARIS_2/tree/release.git - git_url: https://github.com/saccharis/SACCHARIS_2.git - git_tag: v{{ version }} +# git_url: https://github.com/saccharis/SACCHARIS_2.git +# git_tag: v{{ version }} + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz + sha256: 9D393600BC51323FC18CD772F679C8CEA8472EC8DAB4D6DEDCEDC5AAF2461EB5 build: noarch: python # number: {{ data.get('build') }} number: {{ build_no }} - script: {{ PYTHON }} setup.py install +# script: {{ PYTHON }} setup.py install +# added --single-version-externally-managed --record=record.txt args based on bioconda test build feedback + script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: - saccharis = saccharis.CLI:cli_main From ae1285ba582e85f57fad37fdde767490dec1fb16 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 17:09:28 -0700 Subject: [PATCH 04/45] lowercased hash, since it's case-sensitive --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 3b93099e55186..3ccb10c0ca2be 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -12,7 +12,7 @@ source: # git_url: https://github.com/saccharis/SACCHARIS_2.git # git_tag: v{{ version }} url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - sha256: 9D393600BC51323FC18CD772F679C8CEA8472EC8DAB4D6DEDCEDC5AAF2461EB5 + sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 build: noarch: python From a7ddfe6bb23706f061bb2cac6a4ca51788b7dbb2 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 17:30:18 -0700 Subject: [PATCH 05/45] added filename as "fn: saccharis-{{ version }}.tar.gz" --- recipes/saccharis/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 3ccb10c0ca2be..ecd9da678b775 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -11,6 +11,7 @@ package: source: # git_url: https://github.com/saccharis/SACCHARIS_2.git # git_tag: v{{ version }} + fn: saccharis-{{ version }}.tar.gz url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 From ebbdbc4fd73c9a93ddd5fcdbd2add52805d01d15 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 19:37:45 -0700 Subject: [PATCH 06/45] removed filename since bioconda considers it an error --- recipes/saccharis/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index ecd9da678b775..3ccb10c0ca2be 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -11,7 +11,6 @@ package: source: # git_url: https://github.com/saccharis/SACCHARIS_2.git # git_tag: v{{ version }} - fn: saccharis-{{ version }}.tar.gz url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 From 3e3a965f2792db135223e26d4c56cdaaaa01ac5a Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 20:22:51 -0700 Subject: [PATCH 07/45] update url link --- recipes/saccharis/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 3ccb10c0ca2be..2cfba645a4cae 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -11,7 +11,9 @@ package: source: # git_url: https://github.com/saccharis/SACCHARIS_2.git # git_tag: v{{ version }} - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz +# url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz +# urk: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v2.0.0.dev18.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 build: From 4696ace3c7fe009bdcf9de2accc8e85ecf195314 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 23 Jun 2023 20:41:23 -0700 Subject: [PATCH 08/45] update sha256 --- recipes/saccharis/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 2cfba645a4cae..9141c6f0ad8ae 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -12,10 +12,11 @@ source: # git_url: https://github.com/saccharis/SACCHARIS_2.git # git_tag: v{{ version }} # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz -# urk: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v2.0.0.dev18.tar.gz +# url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v2.0.0.dev18.tar.gz url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 - +# sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 + sha256: 6d3f2818853d812a00c6203cea0b6667b086df846f518591cb5f0469c4dda778 + build: noarch: python # number: {{ data.get('build') }} From e68ac6270611210f8a03d644e4757aba84e7f41c Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Mon, 26 Jun 2023 13:21:30 -0700 Subject: [PATCH 09/45] remove unneeded comments --- recipes/saccharis/meta.yaml | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 9141c6f0ad8ae..2d1d9288a80f3 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,28 +1,18 @@ -#{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %} {% set name = "SACCHARIS" %} {% set version = "2.0.0.dev18" %} {% set build_no = 0 %} package: name: "{{ name|lower }}" -# version: {{ data.get('version') }} version: "{{ version }}" source: -# git_url: https://github.com/saccharis/SACCHARIS_2.git -# git_tag: v{{ version }} -# url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz -# url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v2.0.0.dev18.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz -# sha256: 9d393600bc51323fc18cd772f679c8cea8472ec8dab4d6dedcedc5aaf2461eb5 + url: "https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz" sha256: 6d3f2818853d812a00c6203cea0b6667b086df846f518591cb5f0469c4dda778 build: noarch: python -# number: {{ data.get('build') }} number: {{ build_no }} -# script: {{ PYTHON }} setup.py install -# added --single-version-externally-managed --record=record.txt args based on bioconda test build feedback script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: From a5b62b4845ea2748ffb700852cad2dbddb00f643 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Mon, 26 Jun 2023 13:39:56 -0700 Subject: [PATCH 10/45] remove tests which write files --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 2d1d9288a80f3..340d2ef161d9f 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -64,8 +64,8 @@ test: commands: #future todo: pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests - saccharis -v - - saccharis.make_family_files - - saccharis.show_family_categories +# - saccharis.make_family_files +# - saccharis.show_family_categories about: home: https://github.com/saccharis/SACCHARIS_2 From f2ff867652726afbbec4d7b2907cbf6aed89f485 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Mon, 26 Jun 2023 13:41:27 -0700 Subject: [PATCH 11/45] remove tests which write files, with comment --- recipes/saccharis/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 340d2ef161d9f..559c399eb7971 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -64,6 +64,7 @@ test: commands: #future todo: pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests - saccharis -v +# below tests write files to disk, which breaks bioconda automated test harness because it lacks write permissions # - saccharis.make_family_files # - saccharis.show_family_categories From 83b518b918469b6d19342357a618e531b0397b9d Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Wed, 23 Aug 2023 16:40:40 -0700 Subject: [PATCH 12/45] add new release data to bioconda recipe --- recipes/saccharis/meta.yaml | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 559c399eb7971..e404fc0f10aee 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,15 +1,16 @@ - {% set name = "SACCHARIS" %} - {% set version = "2.0.0.dev18" %} - {% set build_no = 0 %} +{% set name = "SACCHARIS" %} + {% set version = "2.0.0.dev19" %} + {% set build_no = 7 %} + {% set hash = "1055846A2123B34699B6E93AFCBCCD7B04633DC385DA60E784504D67FDCAA01C" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 6d3f2818853d812a00c6203cea0b6667b086df846f518591cb5f0469c4dda778 - + url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ hash|lower }} + build: noarch: python number: {{ build_no }} @@ -24,6 +25,7 @@ build: - saccharis.screen_cazome = saccharis.ScreenUserFile:cli_cazome - saccharis.show_family_categories = saccharis.utils.FamilyCategories:show_categories - saccharis-gui = saccharis.gui.PipelineGUI:main + - saccharis.config = saccharis.utils.AdvancedConfig:cli_config requirements: build: @@ -34,11 +36,12 @@ requirements: run: - beautifulsoup4 >=4.11.1 - biopython >=1.79 - - dbcan >=3.0.6, < 4 # [not win] + - dbcan >=3.0.6, < 4 - diamond >=2.0.15 # [not win] - fasttree >=2.1.11 # [not win] - hmmer >=3.3 # [not win] - lxml >=4.9.0 + - ncbi-datasets-pylib >=14.* - modeltest-ng >=0.1.7 # [not win] - muscle >=3.8 # [not win] - psutil @@ -62,11 +65,11 @@ app: test: commands: - #future todo: pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests - - saccharis -v -# below tests write files to disk, which breaks bioconda automated test harness because it lacks write permissions + # pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests + - saccharis -v > /dev/null + - saccharis.show_family_categories > /dev/null +# below tests need to be commented out for successful build on bioconda because there is no file write permission # - saccharis.make_family_files -# - saccharis.show_family_categories about: home: https://github.com/saccharis/SACCHARIS_2 From 7e31b9676232399c891fab877d03a951836bc3d7 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Wed, 23 Aug 2023 19:53:53 -0700 Subject: [PATCH 13/45] change build number to zero to satisfy bioconda linter --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index e404fc0f10aee..05b91256e6be5 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.0.dev19" %} - {% set build_no = 7 %} + {% set build_no = 0 %} # actually build 7, but previous dev19 builds were not uploaded to bioconda {% set hash = "1055846A2123B34699B6E93AFCBCCD7B04633DC385DA60E784504D67FDCAA01C" %} package: From 9ab5ebd10f98b5dbf2644d10d231d16cbf9ada94 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 11:29:35 -0700 Subject: [PATCH 14/45] add blast dependency --- recipes/saccharis/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 05b91256e6be5..20fa341c8dc1e 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.0.dev19" %} - {% set build_no = 0 %} # actually build 7, but previous dev19 builds were not uploaded to bioconda + {% set build_no = 7 %} # actually build 7, but previous dev19 builds were not uploaded to bioconda {% set hash = "1055846A2123B34699B6E93AFCBCCD7B04633DC385DA60E784504D67FDCAA01C" %} package: @@ -36,6 +36,7 @@ requirements: run: - beautifulsoup4 >=4.11.1 - biopython >=1.79 + - blast >= 2.* - dbcan >=3.0.6, < 4 - diamond >=2.0.15 # [not win] - fasttree >=2.1.11 # [not win] From 84a1857709c340d6eea829dc4702ddc02384f533 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 11:49:09 -0700 Subject: [PATCH 15/45] add run_exports breaking change behaviour --- recipes/saccharis/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 20fa341c8dc1e..627b696c8f57a 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -26,6 +26,8 @@ build: - saccharis.show_family_categories = saccharis.utils.FamilyCategories:show_categories - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config + run_exports: + - { { pin_subpackage({{ name }}, max_pin="x.x") } } requirements: build: From bc0d6d15ab7ada6fb3249aae313a6f4e8da3444f Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 12:10:46 -0700 Subject: [PATCH 16/45] change name to lowercase in run_exports --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 627b696c8f57a..87e6b43f1f540 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -27,7 +27,7 @@ build: - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config run_exports: - - { { pin_subpackage({{ name }}, max_pin="x.x") } } + - { { pin_subpackage({{ name|lower }}, max_pin="x.x") } } requirements: build: From d4eeb44231cc70f27248e420d7cfcb4ee76117e9 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 12:11:44 -0700 Subject: [PATCH 17/45] fix spacing --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 87e6b43f1f540..90a3be4c28f5b 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -27,7 +27,7 @@ build: - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config run_exports: - - { { pin_subpackage({{ name|lower }}, max_pin="x.x") } } + - {{ pin_subpackage({{ name|lower }}, max_pin="x.x") }} requirements: build: From f59a507d68fce5989334a5ec43a226d440a52a39 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 12:26:44 -0700 Subject: [PATCH 18/45] nesting issue --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 90a3be4c28f5b..87e6b43f1f540 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -27,7 +27,7 @@ build: - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config run_exports: - - {{ pin_subpackage({{ name|lower }}, max_pin="x.x") }} + - { { pin_subpackage({{ name|lower }}, max_pin="x.x") } } requirements: build: From 6d75ac28e7ab0bb66a57353fa9aef95752715131 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 14:03:23 -0700 Subject: [PATCH 19/45] remove nesting --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 87e6b43f1f540..03a953f237db4 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -27,7 +27,7 @@ build: - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config run_exports: - - { { pin_subpackage({{ name|lower }}, max_pin="x.x") } } + - {{ pin_subpackage("saccharis", max_pin="x.x") }} requirements: build: From df74506b0ddfed62156ce895f65d3fac11363ed2 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 29 Aug 2023 14:42:06 -0700 Subject: [PATCH 20/45] fix version spacing --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 03a953f237db4..6ecd68c9dffa8 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -38,7 +38,7 @@ requirements: run: - beautifulsoup4 >=4.11.1 - biopython >=1.79 - - blast >= 2.* + - blast >=2.* - dbcan >=3.0.6, < 4 - diamond >=2.0.15 # [not win] - fasttree >=2.1.11 # [not win] From e6a01df862d9648636a686cdfff307de25268851 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 8 Sep 2023 11:15:49 -0700 Subject: [PATCH 21/45] update to dev20 --- recipes/saccharis/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 6ecd68c9dffa8..98ab15113079d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,14 +1,14 @@ {% set name = "SACCHARIS" %} - {% set version = "2.0.0.dev19" %} - {% set build_no = 7 %} # actually build 7, but previous dev19 builds were not uploaded to bioconda - {% set hash = "1055846A2123B34699B6E93AFCBCCD7B04633DC385DA60E784504D67FDCAA01C" %} + {% set version = "2.0.0.dev20" %} + {% set build_no = 0 %} + {% set hash = "E56B68C7CC168CCD02E91C60BEDEC6CC2259E47972CF515100C3F261E5086B34" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/saccharis/SACCHARIS_2/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz sha256: {{ hash|lower }} build: @@ -26,6 +26,8 @@ build: - saccharis.show_family_categories = saccharis.utils.FamilyCategories:show_categories - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config + - saccharis.update_db = saccharis.ExtractAndPruneCAZymes:update_hmms + run_exports: - {{ pin_subpackage("saccharis", max_pin="x.x") }} From 5ffd64f2977ebd6c87588a0bf44fe6afd06d1b93 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 8 Sep 2023 11:59:20 -0700 Subject: [PATCH 22/45] update to dev20 --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 98ab15113079d..509b42a3e2c0c 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -79,7 +79,7 @@ test: about: home: https://github.com/saccharis/SACCHARIS_2 dev_url: https://github.com/saccharis/SACCHARIS_2 - description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences + description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences via creation of phylogenetic trees. license: GPL v3 license_file: LICENSE - summary: A CAZyme discovery tool. + summary: A CAZyme discovery tool. Easily create phylogenetic trees from FASTA files and CAZyme families. From f234ecde405ee37f30b827ae9cb6cf4c22a0dc55 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Wed, 20 Sep 2023 14:02:56 -0700 Subject: [PATCH 23/45] update to dev21 --- recipes/saccharis/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 02466ba01d2fc..774824429f0b7 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,7 +1,7 @@ {% set name = "SACCHARIS" %} - {% set version = "2.0.0.dev20" %} + {% set version = "2.0.0.dev21" %} {% set build_no = 0 %} - {% set hash = "E56B68C7CC168CCD02E91C60BEDEC6CC2259E47972CF515100C3F261E5086B34" %} + {% set hash = "7D505CF1B0D441E0A2492AE8421250E0FFC98E14480AD25DC232332D8FD4E29D" %} package: @@ -55,6 +55,7 @@ requirements: - python-dotenv >=0.20.0 - python-wget >=3.2 - raxml >=8.2.12 # [not win] + - raxml-ng >= 1.2 # [not win] - requests >=2.28.0 - pyqt >=5,<6 - pyqt5-sip >=12.11 From 4eb40560bfb12e6dcfd8b9e7cb52c31f6e58c40a Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Wed, 20 Sep 2023 14:22:54 -0700 Subject: [PATCH 24/45] fix >= sign --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 774824429f0b7..f821f0e83b50d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -55,7 +55,7 @@ requirements: - python-dotenv >=0.20.0 - python-wget >=3.2 - raxml >=8.2.12 # [not win] - - raxml-ng >= 1.2 # [not win] + - raxml-ng >=1.2 # [not win] - requests >=2.28.0 - pyqt >=5,<6 - pyqt5-sip >=12.11 From 4fb04574095928ccf0433a7a27616b8d78cb5b08 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 21 Sep 2023 19:22:08 -0700 Subject: [PATCH 25/45] increment build to fix small error --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index f821f0e83b50d..3672b43b37a12 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,7 +1,7 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.0.dev21" %} - {% set build_no = 0 %} - {% set hash = "7D505CF1B0D441E0A2492AE8421250E0FFC98E14480AD25DC232332D8FD4E29D" %} + {% set build_no = 1 %} + {% set hash = "9A48463C870E5F3BFB98300A0DB12EE230B110BAEFBE333E1CB2B2022515856C" %} package: From 4e71a6eb7051e6b73f7b4ab9fb0a51f48b820e4e Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 22 Sep 2023 12:18:14 -0700 Subject: [PATCH 26/45] update file hash and increment build --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 3672b43b37a12..e6ebf9c22151a 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,7 +1,7 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.0.dev21" %} - {% set build_no = 1 %} - {% set hash = "9A48463C870E5F3BFB98300A0DB12EE230B110BAEFBE333E1CB2B2022515856C" %} + {% set build_no = 2 %} + {% set hash = "BA68CAB1070A11D5D4F2335CB770E1603ED54E1FB4B52A31DB4CA9A6CBBD6F7E" %} package: From 3e8ddf00c88511dd6612c99ee9853f6ebadbcea5 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 10 Sep 2024 13:06:56 -0700 Subject: [PATCH 27/45] revert 2.0.1 to working dev21 build --- recipes/saccharis/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index dacd35cfbd8fd..9353926ac29f9 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,18 +1,19 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1" %} -{% set hash = "b2bce5fb1d2c959df571735634de5b68fd175148978613e6fc0daa24b3e25df9" %} +{% set hash = "BA68CAB1070A11D5D4F2335CB770E1603ED54E1FB4B52A31DB4CA9A6CBBD6F7E" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz +# url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz # go back to this method once 2.0.1 is fixed + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.0.dev21/saccharis-2.0.0.dev21.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: From b1dfdf8144a671f64c02094b1774671f913d662e Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 17 Sep 2024 17:38:57 -0700 Subject: [PATCH 28/45] upload 2.0.1 dev21 version with fixed database download --- recipes/saccharis/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 9353926ac29f9..ec04a0ed83ab7 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,19 +1,18 @@ {% set name = "SACCHARIS" %} -{% set version = "2.0.1" %} -{% set hash = "BA68CAB1070A11D5D4F2335CB770E1603ED54E1FB4B52A31DB4CA9A6CBBD6F7E" %} +{% set version = "2.0.1.dev21" %} +{% set hash = "1e5c4bb35414d1421f4debcf0ecb53cd62a853b40a887486a44c2c7a8929b113" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: -# url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz # go back to this method once 2.0.1 is fixed - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.0.dev21/saccharis-2.0.0.dev21.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 1 + number: 0 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: From e1f3d312fe5eaef31846f4fb57ed1f5a85529def Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 10 Oct 2024 11:58:34 -0700 Subject: [PATCH 29/45] upload 2.0.1 dev21 version with another database download fix --- recipes/saccharis/meta.yaml | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 6be4f7b7a92d2..804d68b3d706c 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "1e5c4bb35414d1421f4debcf0ecb53cd62a853b40a887486a44c2c7a8929b113" %} +{% set hash = "B4D656E42C87ED46EC555445BBF3EB4496C6463ACE556D9FE0E43A3C1BE2CDB6" %} package: @@ -8,12 +8,13 @@ package: version: "{{ version }}" source: - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz + # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_1.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: @@ -23,10 +24,10 @@ build: - saccharis.rename_user_file = saccharis.utils.UserFastaRename:cli_main - saccharis.prune_seqs = saccharis.ExtractAndPruneCAZymes:cli_prune_seqs - saccharis.screen_cazome = saccharis.ScreenUserFile:cli_cazome - - saccharis.show_family_categories = saccharis.utils.FamilyCategories:show_categories + - saccharis.show_family_categories = saccharis.utils.FamilyCategories:cli_show_categories - saccharis-gui = saccharis.gui.PipelineGUI:main - saccharis.config = saccharis.utils.AdvancedConfig:cli_config - - saccharis.update_db = saccharis.ExtractAndPruneCAZymes:update_hmms + - saccharis.update_db = saccharis.utils.DatabaseDownload:cli_update_hmms run_exports: - {{ pin_subpackage("saccharis", max_pin="x.x") }} @@ -71,13 +72,19 @@ test: # pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests - saccharis -v > /dev/null - saccharis.show_family_categories > /dev/null -# below tests need to be commented out for successful build on bioconda because there is no file write permission -# - saccharis.make_family_files + - saccharis.make_family_files --help > /dev/null + - saccharis.add_family_category --help > /dev/null + - saccharis.rename_user_file --help > /dev/null + - saccharis.prune_seqs --help > /dev/null + - saccharis.screen_cazome --help > /dev/null + - saccharis.config --help > /dev/null + - saccharis.update_db --help > /dev/null about: home: https://github.com/saccharis/SACCHARIS_2 dev_url: https://github.com/saccharis/SACCHARIS_2 - description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences via creation of phylogenetic trees. + description: Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences via + creation of phylogenetic trees. license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE From ea9b2a33567313002477e8f13268a2f01b960e41 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 10 Oct 2024 16:00:29 -0700 Subject: [PATCH 30/45] increment build num --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 804d68b3d706c..bb99723889fc5 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: From 331bc9527a77d8bf8c3ef4717a9fde1f50032b97 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 10 Oct 2024 16:05:12 -0700 Subject: [PATCH 31/45] increment build num --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index bb99723889fc5..ef2d3214e4d3d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "B4D656E42C87ED46EC555445BBF3EB4496C6463ACE556D9FE0E43A3C1BE2CDB6" %} +{% set hash = "06A0F86DDAB8C870EE526E6DDC2C8E0E344616ACD3F6E0A2D7B41483013B43E2" %} package: @@ -9,7 +9,7 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_1.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_2.tar.gz sha256: {{ hash|lower }} build: From 0ed7835229f07957b21a6dfd2a55907ec0f50f5d Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 10 Oct 2024 16:46:12 -0700 Subject: [PATCH 32/45] increment build num --- recipes/saccharis/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index ef2d3214e4d3d..84c627e4fc1da 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -32,6 +32,9 @@ build: - {{ pin_subpackage("saccharis", max_pin="x.x") }} requirements: + build: + - python + - setuptools host: - python >=3.6 - pip From 52e9f1b4482793a26a485e32c641bbd679ad445c Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 10 Oct 2024 23:58:14 -0700 Subject: [PATCH 33/45] update setuptools build requirements --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 84c627e4fc1da..ff46ad9002413 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "06A0F86DDAB8C870EE526E6DDC2C8E0E344616ACD3F6E0A2D7B41483013B43E2" %} +{% set hash = "327FCE45E7B50BF0C52064DA883CC4A21BCE183EBACF4C4A827FE2C5BE934CB3" %} package: @@ -74,7 +74,7 @@ test: commands: # pipe test output to null for these tests, per https://bioconda.github.io/contributor/guidelines.html#tests - saccharis -v > /dev/null - - saccharis.show_family_categories > /dev/null + - saccharis.show_family_categories --help > /dev/null - saccharis.make_family_files --help > /dev/null - saccharis.add_family_category --help > /dev/null - saccharis.rename_user_file --help > /dev/null From cc77e984d215c3631a2a478b90ec0783107b8627 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 11 Oct 2024 00:31:10 -0700 Subject: [PATCH 34/45] update setuptools build requirements --- recipes/saccharis/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index ff46ad9002413..9fc2b851b8369 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -37,6 +37,7 @@ requirements: - setuptools host: - python >=3.6 + - setuptools - pip run: - beautifulsoup4 >=4.11.1 From 799a23c0350ada4cd3555b3045ac1e8c1d7a4f24 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 25 Oct 2024 18:29:11 -0700 Subject: [PATCH 35/45] update to build 3, which replaces wget with requests --- recipes/saccharis/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 9fc2b851b8369..537cef357fc8d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "327FCE45E7B50BF0C52064DA883CC4A21BCE183EBACF4C4A827FE2C5BE934CB3" %} +{% set hash = "1175A34290C3E52843D9F1F02FB8E4CB4929714FE56EF051C37432671C864745" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_2.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_3.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: @@ -54,7 +54,6 @@ requirements: - psutil - python >=3.8 - python-dotenv >=0.20.0 - - python-wget >=3.2 - raxml >=8.2.12 # [not win] - raxml-ng >=1.2 # [not win] - requests >=2.28.0 From a1c2b90a841d2d258146af8260859e9499d249db Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Fri, 25 Oct 2024 20:00:09 -0700 Subject: [PATCH 36/45] update hash --- recipes/saccharis/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 537cef357fc8d..de48fd85a18ff 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "1175A34290C3E52843D9F1F02FB8E4CB4929714FE56EF051C37432671C864745" %} +{% set hash = "B83DC6502A3AB136D1E5F43E4E66CD41A7B884C99B190B781691C56A6D71998F" %} package: From a8514ca126eeb60c2fa3b93fdffb90c900ff223c Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 31 Oct 2024 12:47:14 -0700 Subject: [PATCH 37/45] increment build with yet another small patch to try and fix these database downloads --- recipes/saccharis/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index de48fd85a18ff..69a2b3dfb6f5f 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,7 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "B83DC6502A3AB136D1E5F43E4E66CD41A7B884C99B190B781691C56A6D71998F" %} - +{% set hash = "90806FDA7473C4687165277FB7765F201B2E3CE5254B43A0FBC8FBCD8C9B8849" %} package: name: "{{ name|lower }}" @@ -9,12 +8,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_3.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_4.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: From f78e12732c85ee641dc00bf2e932594f799aeff0 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Mon, 4 Nov 2024 11:07:36 -0800 Subject: [PATCH 38/45] increment build with yet another small patch to try and fix database downloads --- recipes/saccharis/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 9a871bb5fb6af..fdba970b1329c 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "90806FDA7473C4687165277FB7765F201B2E3CE5254B43A0FBC8FBCD8C9B8849" %} +{% set hash = "551DE1D7B666A5AD693DD61F58A2617BAB3F708836D0143A7FBB981365F45AF4" %} package: @@ -9,13 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_4.tar.gz - + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_5.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 4 + number: 5 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error entry_points: From 2a56a958c79bd4b50d0b6772eab3cd70ae934c19 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Mon, 4 Nov 2024 11:11:15 -0800 Subject: [PATCH 39/45] adjust whitespace --- recipes/saccharis/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 44faaf6cdfcf1..881bc4b84bda7 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -3,7 +3,6 @@ {% set hash = "551DE1D7B666A5AD693DD61F58A2617BAB3F708836D0143A7FBB981365F45AF4" %} - package: name: "{{ name|lower }}" version: "{{ version }}" From 788a3777d41c755bbeedfdff21729443ccdd4684 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 5 Nov 2024 13:04:06 -0800 Subject: [PATCH 40/45] increment to build 6 --- recipes/saccharis/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 881bc4b84bda7..ea1cc59fd9907 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "551DE1D7B666A5AD693DD61F58A2617BAB3F708836D0143A7FBB981365F45AF4" %} +{% set hash = "9C58E73A2CEFE90FA2E9744E9A912CA53E383D7F587C1A2516B3E57BF14C86F9" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_5.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_6.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 5 + number: 6 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error From 806599f3cd8a59ec35eb608f50e2ba81bdd17358 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 5 Nov 2024 13:29:02 -0800 Subject: [PATCH 41/45] update python dependency --- recipes/saccharis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index ea1cc59fd9907..7783216ba71b5 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -37,7 +37,7 @@ requirements: - python - setuptools host: - - python >=3.6 + - python >=3.11 - setuptools - pip run: @@ -53,7 +53,7 @@ requirements: - modeltest-ng >=0.1.7 # [not win] - muscle >=3.8 # [not win] - psutil - - python >=3.8 + - python >=3.11 - python-dotenv >=0.20.0 - raxml >=8.2.12 # [not win] - raxml-ng >=1.2 # [not win] From 2928fa4d7a82185675e595adb0b3cd2167d083d3 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 5 Nov 2024 18:59:02 -0800 Subject: [PATCH 42/45] increment to build 7 adds chunk reducing size to database download streaming --- recipes/saccharis/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 7783216ba71b5..5dd7db2b51e4d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "9C58E73A2CEFE90FA2E9744E9A912CA53E383D7F587C1A2516B3E57BF14C86F9" %} +{% set hash = "DEFE4B98CFF4F5ED58A102D7FFE0CC219C4EC44C257AC0469255CDC73F124F57" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_6.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_7.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 6 + number: 7 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error From 4031ee7cd332dd815c6bb5e031ccf4ba4913a3a9 Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Thu, 14 Nov 2024 12:14:32 -0800 Subject: [PATCH 43/45] update cazy.org links to https increment to build 8 --- recipes/saccharis/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 5dd7db2b51e4d..dc9c7a06898df 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "DEFE4B98CFF4F5ED58A102D7FFE0CC219C4EC44C257AC0469255CDC73F124F57" %} +{% set hash = "C808429EADDAA31E0E611DF0564BA6CA36CE6CBB69A98DFB79CC59972352FD16" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_7.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_8.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 7 + number: 8 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error From 6dedbf94358cb2b3c55025bcd5eff18ca0442c3c Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Tue, 19 Nov 2024 16:19:39 -0800 Subject: [PATCH 44/45] fix error on duplicate user ids in different files increment to build 9 --- recipes/saccharis/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index dc9c7a06898df..804d07d108d74 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "C808429EADDAA31E0E611DF0564BA6CA36CE6CBB69A98DFB79CC59972352FD16" %} +{% set hash = "0CC50F3A1D80C4FC8F84783A46E122BC4E382E00B8AD15EF10E985AAF100F43B" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_8.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_9.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 8 + number: 9 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error From 61a49d0bf838fc1a4a53c900d82526b348bc430e Mon Sep 17 00:00:00 2001 From: AlexSCFraser Date: Wed, 20 Nov 2024 15:56:42 -0800 Subject: [PATCH 45/45] update to next public release as version 2.0.2 fix error on duplicate user ids in different files --- recipes/saccharis/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 804d07d108d74..19ba4da41cbf1 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} -{% set version = "2.0.1.dev21" %} -{% set hash = "0CC50F3A1D80C4FC8F84783A46E122BC4E382E00B8AD15EF10E985AAF100F43B" %} +{% set version = "2.0.2" %} +{% set hash = "0405C796154469E0AE8282C0EF51142ADAE0B26E83BDEAF00B9A092063C34F85" %} package: @@ -8,13 +8,12 @@ package: version: "{{ version }}" source: - # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_9.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 9 + number: 0 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error