Merge branch 'master' into bulk

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

recipes/gpatch/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "GPatch" %}
-{% set version = "0.3.5" %}
+{% set version = "0.3.6" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 1443daef746825d0749b7870f6b9e49d874ac4d057486d934f702abd194c52c1
+  sha256: 01246204a200f2e8d497e97876de5f67405bee6a847b967a4107e4b271846391
 
 build:
   number: 0

recipes/hybpiper/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "hybpiper" %}
-{% set version = "2.3.1" %}
+{% set version = "2.3.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: "https://github.com/mossmatters/HybPiper/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 0f341fb26dffd39c13b3bfc5c1d568936bcd0edbe9064399e4aa947d5882d220
+  sha256: ca59cfd837606d28de093dd6603175e3dc6452fc3e7957521defe7ae281b5acc
 
 build:
   number: 0

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:

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

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

recipes/quatradis/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "1.3.1" %}
+{% set version = "1.3.2" %}
 
 package:
   name: quatradis
   version: {{ version }}
 
 source:
   url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 0c05f40e14391b5044aa014cce345e43238ff01d06edfc72258f8608d3796590
+  sha256: 2f37287a97e7721a2f127373ea5ae67e147215aa91e73729133c3746fde2a0fa
 
 build:
   number: 1

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

recipes/samrefiner/meta.yaml

@@ -1,22 +1,25 @@
-{% set version = "1.4" %}
+{% set version = "1.4.1" %}
 
 package:
   name: samrefiner
   version: '{{ version }}'
 
 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
 

recipes/snakemake-executor-plugin-slurm/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "snakemake-executor-plugin-slurm" %}
-{% set version = "0.11.2" %}
+{% set version = "0.12.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz
-  sha256: fca29038d78387c237afb4ec2b04638e6128d2456940dd7b96ac4205f319d7f3
+  sha256: 7069590060e914afcd608c75aee8ccf1128f662dda3e258a84f3c83302232763
 
 build:
   noarch: python

recipes/snakemake/meta.yaml

@@ -1,15 +1,15 @@
 # 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 }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz
-  sha256: b52390cd6c3b591e5c4a0977df93d8f25a4a38a5c43dee4c7e2093393cb1f053
+  sha256: 7bee7e4f255fd75738b6840c3453c9b5a4f33c628705c38a5a462db008f0334d
 
 build:
   number: 0