Add azimuth and dependencies (bioconda#45914)

* Add azimuth and dependencies * Use github archives and add run_exports * fix run_exports * rename to have r- prefix * SPDX
Tim15-tech · Apr 3, 2024 · 29e82fb · 29e82fb
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diff --git a/recipes/r-azimuth/meta.yaml b/recipes/r-azimuth/meta.yaml
@@ -0,0 +1,86 @@
+{% set version = '0.4.6' %}
+package:
+  name: r-azimuth
+  version: {{ version|replace("-", "_") }}
+source:
+  url: https://github.com/satijalab/azimuth/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 14f2c307590dec6184702be4042f62def674b91f75af5153a6ae0d89277f5fd2
+build:
+  script: $R CMD INSTALL --build .
+  run_exports:
+    - {{ pin_subpackage("r-azimuth", max_pin="x.x.x") }}
+  number: 0
+  rpaths:
+    - lib/R/lib/
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - r-base
+    - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0'
+    - 'r-dt >=0.15'
+    - 'r-matrix >=1.2.18'
+    - 'r-rcpp >=1.0.7'
+    - 'r-seurat >=4.0.0'
+    - 'r-seurat-data ==0.2.1'
+    - 'r-seurat-disk ==0.0.0.9021'
+    - 'r-seuratobject'
+    - 'r-future >=1.19.1'
+    - 'r-ggplot2 >=3.3.2'
+    - 'bioconductor-glmgampoi >=1.0.0'
+    - 'r-googlesheets4 >=0.2.0'
+    - 'r-hdf5r >=1.3.2'
+    - 'r-htmltools >=0.5.0'
+    - 'r-httr >=1.4.2'
+    - 'r-jsonlite >=1.7.0'
+    - 'r-patchwork >=1.0.1'
+    - 'r-plotly'
+    - 'r-presto ==1.0.0'
+    - 'r-rlang >=0.4.8'
+    - 'r-scales >=1.1.1'
+    - 'r-shiny >=1.5.0'
+    - 'r-shinybs >=0.61'
+    - 'r-shinydashboard >=0.7.1'
+    - 'r-shinyjs >=2.0.0'
+    - 'r-stringr >=1.4.0'
+    - 'r-withr >=2.3.0'
+  run:
+    - r-base
+    - 'r-dt >=0.15'
+    - 'r-matrix >=1.2.18'
+    - 'r-rcpp >=1.0.7'
+    - 'r-seurat >=4.0.0'
+    - 'r-seurat-data ==0.2.1'
+    - 'r-seurat-disk ==0.0.0.9021'
+    - 'r-seuratobject'
+    - 'r-future >=1.19.1'
+    - 'r-ggplot2 >=3.3.2'
+    - 'bioconductor-glmgampoi >=1.0.0'
+    - 'r-googlesheets4 >=0.2.0'
+    - 'r-hdf5r >=1.3.2'
+    - 'r-htmltools >=0.5.0'
+    - 'r-httr >=1.4.2'
+    - 'r-jsonlite >=1.7.0'
+    - 'r-patchwork >=1.0.1'
+    - 'r-plotly'
+    - 'r-presto ==1.0.0'
+    - 'r-rlang >=0.4.8'
+    - 'r-scales >=1.1.1'
+    - 'r-shiny >=1.5.0'
+    - 'r-shinybs >=0.61'
+    - 'r-shinydashboard >=0.7.1'
+    - 'r-shinyjs >=2.0.0'
+    - 'r-stringr >=1.4.0'
+    - 'r-withr >=2.3.0'
+test:
+  commands:
+    - '$R -e "library(''Azimuth'')"'
+about:
+  home: https://github.com/satijalab/azimuth
+  license: GPL-3.0-only
+  summary: Azimuth is a Shiny app demonstrating a query-reference mapping algorithm for single-cell data.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+    - LICENSE
diff --git a/recipes/r-presto/meta.yaml b/recipes/r-presto/meta.yaml
@@ -0,0 +1,54 @@
+{% set version = '1.0.0' %}
+package:
+  name: r-presto
+  version: {{ version|replace("-", "_") }}
+source:
+  url: https://github.com/immunogenomics/presto/archive/31dc97fed5e2e7fc323ae4af62f72181cc51d9a3.tar.gz
+  sha256: 720ef58aba219af03344e0ae0408fc48feda50e6b7f7f4af2251eb24ce1bfb88
+build:
+  script: $R CMD INSTALL --build .
+  run_exports:
+    - {{ pin_subpackage("r-presto", max_pin="x.x.x") }}
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+# Suggests: knitr, rmarkdown, testthat, Seurat, SingleCellExperiment, SummarizedExperiment, broom, BiocStyle, DESeq2
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - r-base
+    - r-matrix
+    - r-rcpp
+    - r-rcpparmadillo
+    - r-data.table
+    - r-dplyr
+    - r-purrr
+    - r-rlang
+    - r-tibble
+    - r-tidyr
+  run:
+    - r-base
+    - r-matrix
+    - r-rcpp
+    - r-rcpparmadillo
+    - r-data.table
+    - r-dplyr
+    - r-purrr
+    - r-rlang
+    - r-tibble
+    - r-tidyr
+test:
+  commands:
+    - $R -e "library('presto')"
+about:
+  home: https://github.com/immunogenomics/presto
+  license: GPL-3.0-only
+  summary: Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces
+    to dense and sparse matrices, as well as genomics analysis frameworks Seurat and
+    SingleCellExperiment.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
diff --git a/recipes/r-seurat-data/meta.yaml b/recipes/r-seurat-data/meta.yaml
@@ -0,0 +1,42 @@
+{% set version = '0.2.1' %}
+package:
+  name: r-seurat-data
+  version: {{ version|replace("-", "_") }}
+source:
+  url: https://github.com/satijalab/seurat-data/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 134b0dbc113e3533494461646c8362189b2bdf8940050de3561bcd488d905438
+build:
+  script: $R CMD INSTALL --build .
+  run_exports:
+    - {{ pin_subpackage("r-seurat-data", max_pin="x.x.x") }}
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+  host:
+    - r-base
+    - r-cli
+    - r-crayon
+    - r-rappdirs
+  run:
+    - r-base
+    - r-cli
+    - r-crayon
+    - r-rappdirs
+test:
+  commands:
+    - $R -e "library('SeuratData')"
+about:
+  home: http://www.satijalab.org/seurat
+  dev_url: https://github.com/satijalab/seurat-data
+  license: GPL-3.0-only
+  summary: Single cell RNA sequencing datasets can be large, consisting of matrices that contain
+    expression data for several thousand features across several thousand cells. This
+    package is designed to easily install, manage, and learn about various single-cell
+    datasets, provided Seurat objects and distributed as independent packages.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+    - LICENSE
diff --git a/recipes/r-seurat-disk/meta.yaml b/recipes/r-seurat-disk/meta.yaml
@@ -0,0 +1,59 @@
+{% set version = '0.0.0.9021' %}
+package:
+  name: r-seurat-disk
+  version: {{ version|replace("-", "_") }}
+source:
+  url: https://github.com/mojaveazure/seurat-disk/archive/877d4e18ab38c686f5db54f8cd290274ccdbe295.tar.gz
+  sha256: d2d6b6604e8a1f6de90956d0401d34b51b07b30671a445d0e06876f2dec999ac
+build:
+  script: $R CMD INSTALL --build .
+  run_exports:
+    - {{ pin_subpackage("r-seurat-disk", max_pin="x.x.x.x") }}
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+  host:
+    - r-base
+    - r-matrix >=1.2.18
+    - r-r6 >=2.4.1
+    - r-seurat >=3.2.0
+    - r-seuratobject >=4.0.0
+    - r-cli >=2.0.1
+    - r-crayon >=1.3.4
+    - r-hdf5r >=1.3.0
+    - r-rlang >=0.4.4
+    - r-stringi >=1.4.6
+    - r-withr >=2.1.2
+  run:
+    - r-base
+    - r-matrix >=1.2.18
+    - r-r6 >=2.4.1
+    - r-seurat >=3.2.0
+    - r-seuratobject >=4.0.0
+    - r-cli >=2.0.1
+    - r-crayon >=1.3.4
+    - r-hdf5r >=1.3.0
+    - r-rlang >=0.4.4
+    - r-stringi >=1.4.6
+    - r-withr >=2.1.2
+test:
+  commands:
+    - '$R -e "library(''SeuratDisk'')"'
+about:
+  home: https://mojaveazure.github.io/seurat-disk/
+  dev_url: https://github.com/mojaveazure/seurat-disk
+  license: GPL-3.0-only
+  summary: The h5Seurat file format is specifically designed for the storage and analysis of
+    multi-modal single-cell and spatially-resolved expression experiments, for example,
+    from CITE-seq or 10X Visium technologies. It holds all molecular information and
+    associated metadata, including (for example) nearest-neighbor graphs, dimensional
+    reduction information, spatial coordinates and image data, and cluster labels. We
+    also support rapid and on-disk conversion between h5Seurat and AnnData objects,
+    with the goal of enhancing interoperability between Seurat and Scanpy.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+    - LICENSE