From 58f96fb355ef2aa5bfdcdcf0a1cbf00d3c5309cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Jan 2025 16:45:34 -0500 Subject: [PATCH 01/11] Update gpatch to 0.3.6 (#53089) --- recipes/gpatch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gpatch/meta.yaml b/recipes/gpatch/meta.yaml index 90a6674ee5a8d..73559f8369bb1 100644 --- a/recipes/gpatch/meta.yaml +++ b/recipes/gpatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GPatch" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1443daef746825d0749b7870f6b9e49d874ac4d057486d934f702abd194c52c1 + sha256: 01246204a200f2e8d497e97876de5f67405bee6a847b967a4107e4b271846391 build: number: 0 From 2c292a5cff6703fff04097127282c594f9c0be2d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Jan 2025 18:05:25 -0500 Subject: [PATCH 02/11] Update quatradis to 1.3.2 (#53090) --- recipes/quatradis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index d06896d5b8edc..d66e518293ca6 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: quatradis @@ -6,7 +6,7 @@ package: source: url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz - sha256: 0c05f40e14391b5044aa014cce345e43238ff01d06edfc72258f8608d3796590 + sha256: 2f37287a97e7721a2f127373ea5ae67e147215aa91e73729133c3746fde2a0fa build: number: 0 From f062af9047ba6be76480c088274c4df08ed1ae77 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Jan 2025 00:35:53 -0500 Subject: [PATCH 03/11] Update hybpiper to 2.3.2 (#53093) --- recipes/hybpiper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml index df405b33da02d..b4366fbb7fec5 100644 --- a/recipes/hybpiper/meta.yaml +++ b/recipes/hybpiper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybpiper" %} -{% set version = "2.3.1" %} +{% set version = "2.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://github.com/mossmatters/HybPiper/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 0f341fb26dffd39c13b3bfc5c1d568936bcd0edbe9064399e4aa947d5882d220 + sha256: ca59cfd837606d28de093dd6603175e3dc6452fc3e7957521defe7ae281b5acc build: number: 0 From e146c3f6e8fdcd9502b22a4a871e5486389662a3 Mon Sep 17 00:00:00 2001 From: Pavel Vazquez Faci <79310152+pavelvazquez@users.noreply.github.com> Date: Wed, 8 Jan 2025 06:42:15 +0100 Subject: [PATCH 04/11] Add PyTorch 2.x (CPU-only) dependency for immuneML (#53088) --- recipes/immuneml/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/immuneml/meta.yaml b/recipes/immuneml/meta.yaml index 4ae3b64f13d44..769e1ef4fbe3a 100644 --- a/recipes/immuneml/meta.yaml +++ b/recipes/immuneml/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 788591fe4d792ede77d5916489d36aab366ceae7ae411fa699b6aea486e9713f build: - number: 0 + number: 1 skip: true # [py<39 or py>311 or target_platform == "osx-64"]# run_exports: - {{ pin_subpackage('immuneml', max_pin="x") }} @@ -52,6 +52,7 @@ requirements: - olga >=1.2.4 - tensorflow >=2.12.0 - keras >=2.12.0 + - pytorch >=2.* cpu_* test: imports: From 25e61f30937041d7b9d4c1a88eb5220bd98616c4 Mon Sep 17 00:00:00 2001 From: Chris Date: Wed, 8 Jan 2025 05:47:03 +0000 Subject: [PATCH 05/11] Add primalbedtools (#53074) --- recipes/primalbedtools/meta.yaml | 46 ++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/primalbedtools/meta.yaml diff --git a/recipes/primalbedtools/meta.yaml b/recipes/primalbedtools/meta.yaml new file mode 100644 index 0000000000000..f934484a08937 --- /dev/null +++ b/recipes/primalbedtools/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "primalbedtools" %} +{% set version = "0.6.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/primalbedtools-{{ version }}.tar.gz + sha256: fe8d656fef3824c9f9af623cdad61a2ee00ca829c5856522b5f5b8a05d8860dc + +build: + entry_points: + - primalbedtools = primalbedtools.main:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('primalbedtools', max_pin="x.x") }} + +requirements: + host: + - python >=3.9,<4.0 + - poetry-core + - pip + run: + - python >=3.9.0,<4.0.0 + +test: + imports: + - primalbedtools + commands: + - pip check + - primalbedtools --help + requires: + - pip + +about: + home: https://github.com/ChrisgKent/primalbedtools + summary: A collection of tools for working with primer.bed files + license: MPL-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - chriskent From 76c06c03fa021220bb7b802fb38c816fbf06ea6a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Jan 2025 01:52:32 -0500 Subject: [PATCH 06/11] Update samrefiner to 1.4.1 (#53087) --- recipes/samrefiner/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/samrefiner/meta.yaml b/recipes/samrefiner/meta.yaml index 52679b68236a4..894dfc315cb49 100644 --- a/recipes/samrefiner/meta.yaml +++ b/recipes/samrefiner/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4" %} +{% set version = "1.4.1" %} package: name: samrefiner @@ -6,17 +6,20 @@ package: source: url: https://github.com/degregory/SAM_Refiner/archive/refs/tags/v{{ version }}.tar.gz - sha256: 'b51f1a783dc8bb6f10670201019ef5e164aedf45859f3c2fd06f48d8aac9c976' + sha256: 'bd6449a4a23e8f6d89769fdb791113274a3f879777f97add9541f8f49c987af9' build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage('samrefiner', max_pin="x") }} requirements: host: - python >=3.7 - pip + - setuptools run: - python >=3.7 From d430dc959cbf44e93bc2f0c031bec353445ea6b1 Mon Sep 17 00:00:00 2001 From: Alvarosmb <82378017+Alvarosmb@users.noreply.github.com> Date: Wed, 8 Jan 2025 07:55:01 +0100 Subject: [PATCH 07/11] Add ExcludonFinder recipe with run_exports (#53079) --- recipes/excludonfinder/meta.yaml | 45 ++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/excludonfinder/meta.yaml diff --git a/recipes/excludonfinder/meta.yaml b/recipes/excludonfinder/meta.yaml new file mode 100644 index 0000000000000..22c2f37ad3dd9 --- /dev/null +++ b/recipes/excludonfinder/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "excludonfinder" %} +{% set version = "0.1.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/Alvarosmb/ExcludonFinder/archive/v{{ version }}.tar.gz + sha256: cc0a4a3c23d99c473563113e693f00511e1f9fc5a77dec2826ee956b32c323e1 + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('excludonfinder', max_pin="x.x") }} + script: + - mkdir -p $PREFIX/bin + - cp scripts/ExcludonFinder $PREFIX/bin/ + - chmod +x $PREFIX/bin/ExcludonFinder + +requirements: + run: + - r-base >=4.1 + - bwa-mem2 >=2.2.1 + - minimap2 >=2.24 + - samtools >=1.15 + - subread >=2.0.1 + - r-dplyr >=1.0.7 + - r-foreach >=1.5.2 + - r-doparallel >=1.0.17 + - r-data.table >=1.14 + - r-biocmanager >=1.30.19 + - bioconductor-rtracklayer >=1.54.0 + - parallel >=20211022 + +test: + commands: + - ExcludonFinder --help + +about: + home: https://github.com/Alvarosmb/ExcludonFinder + license: MIT + license_file: LICENSE + summary: A tool for identifying and analyzing excludons in genomic data using RNA-seq data From 79ad566a605b4682aa3ae799c32f4a0b9e20687b Mon Sep 17 00:00:00 2001 From: Rei Kajitani <65880667+rkajitani@users.noreply.github.com> Date: Wed, 8 Jan 2025 18:48:28 +0900 Subject: [PATCH 08/11] Add IsoRefiner 0.1.0 (#53038) --- recipes/isorefiner/meta.yaml | 54 ++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 recipes/isorefiner/meta.yaml diff --git a/recipes/isorefiner/meta.yaml b/recipes/isorefiner/meta.yaml new file mode 100644 index 0000000000000..5c5b0f8b3ac99 --- /dev/null +++ b/recipes/isorefiner/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "isorefiner" %} +{% set version = "0.1.0" %} +{% set sha256 = "f219a6023eb3f5f6930401c335d4026cf93198753a085b509f15b3abce93b350" %} + + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/rkajitani/IsoRefiner/archive/refs/tags/v{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python + - pip + - setuptools + run: + - python + - bioconductor-bambu >=3.4.0 + - r-biocmanager + - r-xgboost <=1.7.6 + - espresso >=1.3.2 + - isoquant >=3.3.1 + - perl >=5.22.0.1 + - porechop_abi >=0.5.0 + - rnabloom >=2.0.1 + - stringtie >=2.2.1 + - seqkit >=2.4.0 + - gffcompare >=0.12.6 + - gffread >=0.12.7 + - gmap >=2023.07.20 + - samtools >=1.17 + - polars >=0.19.18 + - pysam + +test: + commands: + - isorefiner -h + +about: + home: https://github.com/rkajitani/IsoRefiner + license: MIT + license_file: LICENSE + license_family: MIT + summary: A refinement tool to identify exon-intron structures of transcript (RNA) isoforms using long reads From 961dbaa169e647961857883dc83e1d28ec97d28f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Jan 2025 09:03:38 -0500 Subject: [PATCH 09/11] Update snakemake-executor-plugin-slurm to 0.12.0 (#53098) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 700e7526b5919..7bdd650803dfc 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.11.2" %} +{% set version = "0.12.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: fca29038d78387c237afb4ec2b04638e6128d2456940dd7b96ac4205f319d7f3 + sha256: 7069590060e914afcd608c75aee8ccf1128f662dda3e258a84f3c83302232763 build: noarch: python From 378465a800f13f748a11b38bbcfdb3f85b49aa02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Jan 2025 09:07:28 -0500 Subject: [PATCH 10/11] Update snakemake to 8.27.0 (#53095) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index a6e94629fe41c..4cccf9baeca09 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.26.0" %} +{% set version = "8.27.0" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: b52390cd6c3b591e5c4a0977df93d8f25a4a38a5c43dee4c7e2093393cb1f053 + sha256: 7bee7e4f255fd75738b6840c3453c9b5a4f33c628705c38a5a462db008f0334d build: number: 0 From a536d7fa73d8281389417b12763d0fe050c4b8dc Mon Sep 17 00:00:00 2001 From: Pablo Mata <76519482+Shettland@users.noreply.github.com> Date: Wed, 8 Jan 2025 15:08:55 +0100 Subject: [PATCH 11/11] Add new recipe for relecov-tools (#53097) * Add new recipe for relecov-tools * Add new recipe for relecov-tools. fix --- recipes/relecov-tools/meta.yaml | 69 +++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 recipes/relecov-tools/meta.yaml diff --git a/recipes/relecov-tools/meta.yaml b/recipes/relecov-tools/meta.yaml new file mode 100644 index 0000000000000..02c9f803e148d --- /dev/null +++ b/recipes/relecov-tools/meta.yaml @@ -0,0 +1,69 @@ +{% set name = "relecov-tools" %} +{% set version = "1.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/relecov_tools-{{ version }}.tar.gz + sha256: 283a19a523cb7fc9b735edfd0cbc6293b0af15db0053855ced5fce143d3eecca + +build: + entry_points: + - relecov-tools=relecov_tools.__main__:run_relecov_tools + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_compatible('relecov_tools', max_pin='x.x') }} + +requirements: + host: + - python >=3.7 + - setuptools + - setuptools-scm + - pip + run: + - python >=3.7 + - click + - questionary + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - rich >=10.0.0 + - requests ==2.27.1 + - paramiko >=2.10.1 + - pyyaml ==6.0.1 + - openpyxl >=3.1.2 + - xlsxwriter ==3.2.0 + - bs4 >=0.0.2 + - tabulate + - pandas + - jinja2 >=3.0.0 + - ena-upload-cli + - bio >=1.4.0 + +test: + imports: + - relecov_tools + commands: + - relecov-tools --help + requires: + - pip + +about: + home: https://github.com/BU-ISCIII/relecov-tools + summary: Tools for managing and processing of relecov data. + license: GPL-3.0-or-later + license_file: LICENSE + description: | + Tools for managing and processing of relecov network data, including download, metadata parsing, validation, and update to public databases. + author: Sara Monzon + author_email: smonzon@isciii.es + +extra: + recipe-maintainers: + - saramonzon + - svarona + - Shettland