Add Linux aarch64 build for more Bioconductor packages (#47730)

* Add Linux aarch64 build for more Bioconductor packages - affyio - beclear - bus - ebimage - edger - graph - rhdf5filters - sparsematrixstats Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> * Do not build ebimage for now - it fails on OSX Update edgeR to 4.0.16 Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> --------- Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
bioconda · May 8, 2024 · f0908ab · f0908ab
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Showing 7 changed files with 33 additions and 13 deletions.
diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 9bd1e4acedbf756386f96d4c1ebb21f3
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -36,11 +36,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: 'LGPL (>= 2)'
+  license: 'LGPL-3.0-or-later'
   summary: 'Tools for parsing Affymetrix data files'
   description: 'Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:affyio
     - doi:10.1038/nmeth.3252

diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: bd34703e5a35dfc888f0029395df2c80
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -54,11 +54,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
+  license: 'GPL-3.0-only'
   summary: 'Correction of batch effects in DNA methylation data'
   description: 'Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:beclear
     - doi:10.1371/journal.pone.0159921

diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 788ab26ecf05f0df93667a7c37f564ff
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -38,11 +38,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
+  license: 'GPL-3.0-only'
   summary: 'Gene network reconstruction'
   description: 'This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:bus
     - doi:10.1038/nmeth.3252

diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "4.0.2" %}
+{% set version = "4.0.16" %}
 {% set name = "edgeR" %}
 {% set bioc = "3.18" %}
 
@@ -11,9 +11,9 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 0ba48556be0c95b929db5bbed32923f3
+  md5: 8fb1c6c67e29d299c991d16d0f6c5f5b
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -41,11 +41,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: 'GPL (>=2)'
+  license: 'GPL-3.0-or-later'
   summary: 'Empirical Analysis of Digital Gene Expression Data in R'
   description: 'Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:edger
     - usegalaxy-eu:edger

diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml
@@ -15,7 +15,7 @@ source:
   patches:
     - patch
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -42,6 +42,8 @@ about:
   summary: 'graph: A package to handle graph data structures'
   description: 'A package that implements some simple graph handling capabilities.'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:graph
     - doi:10.1038/nmeth.3252

diff --git a/recipes/bioconductor-rhdf5filters/meta.yaml b/recipes/bioconductor-rhdf5filters/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 3ecb2d30759fee6bde37bbb1f90fbf79
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -43,4 +43,9 @@ about:
   summary: 'HDF5 Compression Filters'
   description: 'Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.'
   license_file: LICENSE
+extra:
+  additional-platforms:
+    - linux-aarch64
+  identifiers:
+    - biotools:{{ name }}
 
diff --git a/recipes/bioconductor-sparsematrixstats/meta.yaml b/recipes/bioconductor-sparsematrixstats/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 4319e6fb04b91467bd08cc4ce2ad609c
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -48,4 +48,9 @@ about:
   summary: 'Summary Statistics for Rows and Columns of Sparse Matrices'
   description: 'High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.'
   license_file: LICENSE
+extra:
+  additional-platforms:
+    - linux-aarch64
+  identifiers:
+    - biotools:{{ name }}