add r-archr (#51295)

* add r-archr * add build.sh * skip build lint * use release; reset build; apply patch * add 0001-cap-threads.patch * patch name * no win * r 4.1 only; tidy quotes * no stdlib func * lint * drop bin patch * squash patch
bioconda · Oct 14, 2024 · 984b675 · 984b675
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diff --git a/recipes/r-archr/build.sh b/recipes/r-archr/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml
@@ -0,0 +1,116 @@
+{% set version = '1.0.2' %}
+{% set github = 'https://github.com/GreenleafLab/ArchR' %}
+{% set posix = 'm2-' if win else '' %}
+
+package:
+  name: r-archr
+  version: {{ version|replace('-', '_') }}
+
+source:
+  url: {{ github }}/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: afe4d82975e9d75018e9ec9fda3d116f34f99ad1d45990cbc5a2be7dea8df352
+  patches:
+    - patches/0001-cap-threads.patch
+
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  run_exports:
+    - {{ pin_subpackage('r-archr', max_pin='x.x') }}
+
+requirements:
+  build:
+    - cross-r-base {{ r_base }}  # [build_platform != target_platform]
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - r-base =4.1
+    - bioconductor-biocgenerics
+    - bioconductor-biostrings
+    - bioconductor-chromvar
+    - bioconductor-complexheatmap
+    - bioconductor-genomicranges
+    - bioconductor-motifmatchr
+    - bioconductor-rhdf5
+    - bioconductor-rsamtools
+    - bioconductor-s4vectors >=0.9.25
+    - bioconductor-summarizedexperiment
+    - r-data.table
+    - r-ggplot2
+    - r-ggrepel
+    - r-gridextra
+    - r-gtable
+    - r-gtools
+    - r-magrittr
+    - r-matrix
+    - r-matrixstats
+    - r-nabor
+    - r-plyr
+    - r-rcpp >=0.12.16
+    - r-stringr
+    - r-uwot
+  run:
+    - r-base =4.1
+    - bioconductor-biocgenerics
+    - bioconductor-biostrings
+    - bioconductor-chromvar
+    - bioconductor-complexheatmap
+    - bioconductor-genomicranges
+    - bioconductor-motifmatchr
+    - bioconductor-rhdf5
+    - bioconductor-rsamtools
+    - bioconductor-s4vectors >=0.9.25
+    - bioconductor-summarizedexperiment
+    - r-data.table
+    - r-ggplot2
+    - r-ggrepel
+    - r-gridextra
+    - r-gtable
+    - r-gtools
+    - r-magrittr
+    - r-matrix
+    - r-matrixstats
+    - r-nabor
+    - r-plyr
+    - r-rcpp >=0.12.16
+    - r-stringr
+    - r-uwot
+
+test:
+  commands:
+    - $R -e "library('ArchR')"
+
+about:
+  home: https://www.archrproject.com
+  dev_url: {{ github }}
+  doc_url: https://www.archrproject.com/bookdown/index.html
+  license: GPL-2.0-or-later
+  summary: This package is designed to streamline scATAC analyses in R.
+  license_family: GPL2
+  license_file:
+    - {{ environ['PREFIX'] }}/lib/R/share/licenses/GPL-2
+    - {{ environ['PREFIX'] }}/lib/R/share/licenses/GPL-3
+
+extra:
+  recipe-maintainers:
+    - jdblischak
+    - mfansler
+
+# Package: ArchR
+# Type: Package
+# Date: 2022-04-03
+# Title: Analyzing single-cell regulatory chromatin in R.
+# Version: 1.0.2
+# Authors@R: c( person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = c("aut","cre")), person("Ryan", "Corces", role = "aut"))
+# Description: This package is designed to streamline scATAC analyses in R.
+# Roxygen: list(markdown = TRUE)
+# License: GPL (>= 2)
+# LinkingTo: Rcpp
+# LazyData: TRUE
+# RoxygenNote: 7.1.2
+# Encoding: UTF-8
+# Imports: ggplot2, SummarizedExperiment, data.table, Matrix, rhdf5, magrittr, S4Vectors (>= 0.9.25), BiocGenerics, Rcpp (>= 0.12.16), matrixStats, plyr, nabor, motifmatchr, chromVAR, uwot, ggrepel, Rsamtools, gtable, gtools, stringr, grid, gridExtra, Biostrings, ComplexHeatmap, GenomicRanges
+# Depends:
+# Collate: 'AllClasses.R' 'AnnotationGenome.R' 'AnnotationPeaks.R' 'ArchRBrowser.R' 'ArchRHeatmap.R' 'ArrowRead.R' 'ArrowUtils.R' 'ArrowWrite.R' 'BulkProjection.R' 'Clustering.R' 'ColorPalettes.R' 'CreateArrow.R' 'DoubletsScores.R' 'Embedding.R' 'FilterCells.R' 'Footprinting.R' 'GRangesUtils.R' 'GgplotUtils.R' 'GlobalDefaults.R' 'GroupCoverages.R' 'HelperUtils.R' 'GroupExport.R' 'Harmony.R' 'HiddenUtils.R' 'Imputation.R' 'InputData.R' 'IntegrativeAnalysis.R' 'IterativeLSI.R' 'LoggerUtils.R' 'MarkerFeatures.R' 'MatrixDeviations.R' 'MatrixFeatures.R' 'MatrixGeneExpression.R' 'MatrixGeneScores.R' 'MatrixTiles.R' 'ModuleScore.R' 'MultiModal.R' 'ProjectMethods.R' 'QualityControl.R' 'RNAIntegration.R' 'RcppExports.R' 'ReproduciblePeakSet.R' 'Trajectory.R' 'ValidationUtils.R' 'VisualizeData.R'
diff --git a/recipes/r-archr/patches/0001-cap-threads.patch b/recipes/r-archr/patches/0001-cap-threads.patch
@@ -0,0 +1,36 @@
+From f512a5eaab8b12ef4c78414ffdf813c7ebc872c5 Mon Sep 17 00:00:00 2001
+From: Mervin Fansler <mervin.fansler@bric.ku.dk>
+Date: Fri, 11 Oct 2024 12:50:25 +0200
+Subject: [PATCH] bugfix threads not capped to threads input
+
+---
+ R/CreateArrow.R      | 2 +-
+ R/MatrixGeneScores.R | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/R/CreateArrow.R b/R/CreateArrow.R
+index ac0be626..08243139 100644
+--- a/R/CreateArrow.R
++++ b/R/CreateArrow.R
+@@ -205,7 +205,7 @@ createArrowFiles <- function(
+   if(subThreading){
+     h5disableFileLocking()
+   }else{
+-    args$threads <- length(inputFiles)
++    args$threads <- min(length(inputFiles), threads)
+   }
+
+   args$minTSS <- NULL
+diff --git a/R/MatrixGeneScores.R b/R/MatrixGeneScores.R
+index 1d1d10b3..fd342a1a 100644
+--- a/R/MatrixGeneScores.R
++++ b/R/MatrixGeneScores.R
+@@ -125,7 +125,7 @@ addGeneScoreMatrix <- function(
+   if(subThreading){
+     h5disableFileLocking()
+   }else{
+-    args$threads <- length(ArrowFiles)
++    args$threads <- min(length(ArrowFiles), threads)
+   }
+
+   #Remove Input from args