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Add osx-arm64 to biconductor biobase package. #52084

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Add osx-arm64 to biconductor biobase package. #52084

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ff580bd
add arm support for controlfreec
FriederikeHanssen Oct 29, 2024
722fc3e
bump build
rpetit3 Oct 29, 2024
84456c3
Merge branch 'master' into arm_support_cf
mencian Oct 29, 2024
f274933
Update meta.yaml
mencian Oct 29, 2024
719445e
Merge branch 'master' into arm_support_cf
FriederikeHanssen Oct 30, 2024
41fce3d
add debug to build.sh
rpetit3 Oct 30, 2024
c4c2bff
Merge remote-tracking branch 'rike/arm_support_cf' into arm_support_c…
dslarm Nov 11, 2024
97c2371
Replace 'which' with test -x to overcome path length issue in which f…
dslarm Nov 11, 2024
97a3acb
* Add osx-arm64 to meta.yaml
dslarm Nov 13, 2024
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1 change: 1 addition & 0 deletions recipes/bioconductor-biobase/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ about:
extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- biotools:biobase

3 changes: 2 additions & 1 deletion recipes/control-freec/build.sh
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@@ -1,5 +1,6 @@
#!/bin/bash

# Debug for ARM build, can remove later
set -x

mkdir -p $PREFIX/bin

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19 changes: 11 additions & 8 deletions recipes/control-freec/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ source:
- perl_shebang.patch

build:
number: 0
number: 1
run_exports:
- {{ pin_subpackage('control-freec', max_pin="x") }}

Expand All @@ -33,16 +33,17 @@ test:
- freec
- freec2bed.pl
- freec2circos.pl
- which get_fasta_lengths.pl
- which makeGraph.R
- which makeGraph_Chromosome.R
- test -x ${PREFIX}/bin/get_fasta_lengths.pl
- test -x ${PREFIX}/bin/makeGraph.R
- test -x ${PREFIX}/bin/makeGraph_Chromosome.R
- vcf2snpFreec.pl
- which assess_significance.R
- which makeGraph2.0.R
- test -x ${PREFIX}/bin/assess_significance.R
- test -x ${PREFIX}/bin/makeGraph2.0.R

about:
home: https://github.com/BoevaLab/FREEC
license: GPL (>=2)
license: GPL-2.0-or-later
license_family: GPL2
summary: |
Copy number and genotype annotation from whole genome and whole exome
sequencing data.
Expand All @@ -54,4 +55,6 @@ extra:
like e.g. freec2bed.pl and freec2circos.pl (see homepage) are available in the
command line as well.
identifiers:
- biotools:freec
- biotools:freec
additional-platforms:
Comment on lines +59 to +60
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💡 Codebase verification

Missing osx-arm64 Platform Support

  • osx-arm64 is not listed in additional-platforms, which may cause build issues on ARM-based macOS systems.
🔗 Analysis chain

Verify ARM platform compatibility

Before adding platform support, we should verify:

  1. All dependencies support the target platforms
  2. No platform-specific code that might break the build
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if dependencies have ARM support
for pkg in perl r-base bioconductor-rtracklayer samtools; do
  echo "Checking $pkg..."
  conda search --json $pkg | jq '.[] | select(.platform == "osx-arm64" or .platform == "linux-aarch64")'
done

Length of output: 1197

Script:

#!/bin/bash
# Search meta.yaml for ARM platform specifications
rg 'osx-arm64|linux-aarch64' recipes/control-freec/meta.yaml

Length of output: 82

- linux-aarch64
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