abyss: prefer system gcc on Linux
and provide alternative test for Linux when column is not installed on the system.master
parent
8a3b58f918
commit
3551ad3826
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@ -28,9 +28,12 @@ class Abyss < Formula
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depends_on "boost" => :build
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depends_on "google-sparsehash" => :build
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depends_on "gcc"
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depends_on "open-mpi"
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on_macos do
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depends_on "gcc"
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end
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fails_with :clang # no OpenMP support
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resource("testdata") do
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@ -53,7 +56,12 @@ class Abyss < Formula
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test do
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testpath.install resource("testdata")
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system "#{bin}/abyss-pe", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
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if which("column")
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system "#{bin}/abyss-pe", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
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else
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# Fix error: abyss-tabtomd: column: not found
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system "#{bin}/abyss-pe", "unitigs", "scaffolds", "k=25", "name=ts", "in=reads1.fastq reads2.fastq"
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end
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system "#{bin}/abyss-fac", "ts-unitigs.fa"
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end
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end
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