Merge branch 'master' into bump/starfish

recipes/fastk/build.sh

@@ -1,16 +1,19 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="-L$SRC_DIR/HTSLIB -L$PREFIX/lib"
 export CFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib"
 export CPPFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib"
 
 # build HTSLIB
 cd HTSLIB
-make lib-static
+make -j"${CPU_COUNT}" lib-static
 cd -
 # build LIBDEFLATE
 cd LIBDEFLATE
-make
+make -j"${CPU_COUNT}"
 cd -
 # build fastk
-make
+make -j"${CPU_COUNT}"
 make install

recipes/fastk/meta.yaml

@@ -13,7 +13,7 @@ source:
     - patch
 
 build:
-  number: 0
+  number: 1
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("fastk", max_pin="x") }}
@@ -36,3 +36,7 @@ about:
   license: https://github.com/thegenemyers/FASTK/blob/master/LICENSE
   summary: FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
   home: https://github.com/thegenemyers/FASTK
+
+extra:
+  additional-platforms:
+    - linux-aarch64

recipes/gafpack/build.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -euo
+
+set -xe
+
+# build statically linked binary with Rust
+export RUST_BACKTRACE=1
+cargo install --verbose --path . --root ${PREFIX} --no-track

recipes/gafpack/meta.yaml

@@ -0,0 +1,38 @@
+{% set name = "gafpack" %}
+{% set version = "0.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 0b78d8047132965c7b0a9b0f3dc26682c1251d08507ebdd98583d9c1b563c758 
+
+build:
+  number: 0
+  run_exports:
+      - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+
+test:
+  commands:
+    - gafpack --help
+
+about:
+  home: https://github.com/pangenome/{{ name }}
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: Convert alignments to pangenome variation graphs to coverage maps
+  dev_url: https://github.com/pangenome/{{ name }}
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - AndreaGuarracino

recipes/longcallr_nn/meta.yaml

@@ -0,0 +1,51 @@
+{% set name = "longcallr_nn" %}
+{% set version = "0.0.1" %}
+{% set hash = "294155357b7165b127fc821b06dcdbeee28c108a0caf442b28992a5a5cc3e583" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://github.com/huangnengCSU/longcallR-nn/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: {{ hash }}
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - longcallR_nn=longcallR_nn.longcallR_nn:main
+  script:
+    - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+
+requirements:
+  host:
+    - pip
+    - python 3.9.*
+  run:
+    - python 3.9.*
+    - numpy 1.21.0
+    - pyyaml
+    - pysam
+    - tensorboardX
+    - pytorch 1.13.*
+    - torchvision
+    - torchmetrics
+
+test:
+  commands:
+    - longcallR_nn --help
+
+about:
+  home: "https://github.com/huangnengCSU/longcallR-nn"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "longcallR_nn is a variant caller specifically designed for long-read RNA-seq data utilizing a ResNet model."
+  dev_url: "https://github.com/huangnengCSU/longcallR-nn"
+
+extra:
+  recipe-maintainers:
+    - huangnengCSU

recipes/merquryfk/build.sh

@@ -1,8 +1,11 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make
+make -j"${CPU_COUNT}"
 mkdir -p $PREFIX/bin
 
 cp HAPmaker  $PREFIX/bin

recipes/merquryfk/meta.yaml

@@ -13,7 +13,7 @@ source:
     - patch
 
 build:
-  number: 0
+  number: 1
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage("merquryfk", max_pin="x") }}
@@ -50,3 +50,7 @@ about:
   license: https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE
   summary: MerquryFK replaces meryl with the FastK k-mer counter suite to considerably speed up analyses.
   home: https://github.com/thegenemyers/MERQURY.FK
+
+extra:
+  additional-platforms:
+    - linux-aarch64

recipes/metabolights-utils/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "metabolights-utils" %}
-{% set version = "1.1.11" %}
+{% set version = "1.1.12" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
-  sha256: 5290c8c269f5ec3c55d5fc5b24c014c815b24391b831af528a0bec0545337e7e
+  sha256: a9f482e77df79e1efa6c4884edd9b66f21ac7267cf2d8aa7bf9c018cc9c08788
 
 build:
   entry_points:

recipes/oakvar/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.11.11" %}
-{% set sha256 = "16ac185b5e26e422111f7d7e568bd602e972ac2a91feeb4ee61a2193d47cd9a7" %}
+{% set version = "2.11.12" %}
+{% set sha256 = "eb979f31a9291c8285d0ec335102455e8ad0210f59ffddf8074b1fabf76061a3" %}
 
 package:
   name: {{ name|lower }}

recipes/pneumo-typer/meta.yaml

@@ -1,17 +1,18 @@
 {% set name = "pneumo-typer" %}
 {% set version = "1.0.2" %}
-{% set sha256 = "5ba1aa25862376d44f612c1f9d25ac9fa9ab76aa10dc88939fb27518bf70e013" %}
+
+{% set sha256 = "755584efcb967c3afe260650af905123f81e192707ee8078ed9d1db22bbfad41" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-    url: https://www.microbialgenomic.cn/temp_dir/pneumo-typer-v{{ version }}.tar.gz
+    url: https://www.microbialgenomic.cn/gz/pneumo-typer-v{{ version }}.tar.gz
     sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage('pneumo-typer', max_pin="x") }}
@@ -41,7 +42,7 @@ test:
 
 about:
   home: 'https://www.microbialgenomic.cn/Pneumo-Typer.html'
-  summary: 'Pneumo-Typer is a comprehensive prediction and visualization of serotype and sequence type for streptococcus pneumoniae using assembled genomes.'
+  summary: 'Pneumo-Typer: An integrated tool for simultaneous identification of serotype, sequence type, and capsule genotype in Streptococcus pneumoniae.'
   description: 'Pneumo-Typer is a stand-alone perl application, which requires blat, prodigal, NCBI BLAST+, and several perl Modules (GD, GD::SVG) to be installed before use.'
   doc_url: 'https://github.com/Xiangyang1984/Pneumo-Typer'
   license: GNU General Public License v3.0 or any later version (GPL-3.0-or-later)

recipes/r-archr/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+${R} CMD INSTALL --build . ${R_ARGS}

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 = "[email protected]", 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'

recipes/r-archr/patches/0001-cap-threads.patch

@@ -0,0 +1,36 @@
+From f512a5eaab8b12ef4c78414ffdf813c7ebc872c5 Mon Sep 17 00:00:00 2001
+From: Mervin Fansler <[email protected]>
+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