veryfasttree 4.0.4 (new formula) #191023
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veryfasttree 4.0.4 (new formula) #191023
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added
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new formula
carlocab
reviewed
Sep 17, 2024
| end | ||
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| def install | ||
| system "cmake", "-B", "build", *std_cmake_args |
There was a problem hiding this comment.
Let's follow the style used by other formulae:
Suggested change
| system "cmake", "-B", "build", *std_cmake_args | |
| system "cmake", "-S", ".", "-B", "build", *std_cmake_args |
Also, we should really do this:
Suggested change
| system "cmake", "-B", "build", *std_cmake_args | |
| system "cmake", "-S", ".", "-B", "build", "-DUSE_SHARED=ON", "-DUSE_NATIVE=OFF", *std_cmake_args |
USE_SHAREDfollows: https://docs.brew.sh/Acceptable-Formulae#stuff-that-requires-vendored-versions-of-homebrew-formulae- We don't want
USE_NATIVEbecause the binaries we build should be portable.
But even setting USE_SHARED=ON still vendors some stuff (e.g. cli11), when we'd rather it didn't.
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USE_SHARED=ON was created to publish Veryfasttree on Debian without third-party libraries, with the exception of bxzstr and CLI11. bxzstr was excluded because it is not available in the Debian repositories, and CLI11 was excluded because it is a modified version with extended support for certain parameters, allowing Veryfasttree to imitate the FastTree2 CLI syntax.
we can use USE_SHARED=OFF or USE_SHARED=ON with "boost-align, boost-core, boost-sort, bzip2, zlib, robin-map" as dependencies.
This is the debian source repository: https://salsa.debian.org/med-team/veryfasttree
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USE_SHARED=ON with "boost-align, boost-core, boost-sort, bzip2, zlib, robin-map" as dependencies.
Let's do this, please.
You'll probably need
depends_on "robin-map" => :build
depends_on "boost"
uses_from_macos "bzip2"
uses_from_macos "zlib"There was a problem hiding this comment.
Sorry, just realised my initial suggestion had a typo. I meant
USE_SHARED=ON
from the beginning.
carlocab
reviewed
Sep 17, 2024
Comment on lines
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| (testpath/"test.fasta").write(">N3289 | ||
| --RNRSCRRDNTNGQDLQAALAIFAAKVYVGVALQSVQVAAGIGKHPVYKHIPSKKYTGL | ||
| IIQELYLERLMAELADGLADAAPDVLLDIRGLMLALDAPAREKPIIL-LHLAASAGDALR | ||
| DKGQALRRELLPRLSGLGYAGLASGALTGDNATLMSARLIGLLVSATLLAL--------- | ||
| ----------------- | ||
| >N1763 | ||
| ------ISKDTTEERFLEVDKLTFAPKSYAGTLQTKILSAVSVPAGTLYKDFPTTELALL | ||
| VTLEVYQATDTSGAQDGLAANARDILHVLVELFLALAGFAAQDPLHLLLPMAAALTSSLR | ||
| GRLRELRRELLAKGAAKVYTGLGAADATGDGVQLGAASLAMQLLGALLPCLRLDALLGSL | ||
| ASGLPEEKLASLAIFL- | ||
| >N2100 | ||
| --RGRARPKQTTAESNLDATMGKFASQEYDGTMHRELGAASGVSLGTLYPDYPTWEMLIL | ||
| VTLESYLEPVVSALYAGLATDAPDILQR-LQLFLALLGFAMNHPGALLKSLAATLESELC | ||
| GKLKALTREVLEKLGASVFEGLPEPTLTGDEATPMSAALLMPLVQALLLCLLLQPLLAKH | ||
| SDDLPQIILAIYGIF-- | ||
| >N774 | ||
| --RGRRRTKTIVSEKDLSATMGRFAEQPYDGSLERNAATAASAPLNTMYGEFPTQDMFLL | ||
| MCLESYLIPTVLEADAE-ATEARDVLRRRLQLFLALLGFALNHPTQLLKMLATTLHKALR | ||
| GKIKDLQREVFARLTASAPAGLAAQFLTGDNATLMEAVLLMPFLAALLSCLILEPLDRKF | ||
| ADDFPAVILAIYAIF-- | ||
| >N211 | ||
| --KARGRTTIETGEKVLTGEMDRFAELQYDGSLQRDDTTGAAPPLGTLYGKLPTQDMFLL | ||
| FALESYLDPGTPELGQGLATKAPDGLRKRLHLFLGLLSFSLDHPVHLLKSLATT-HKAVR | ||
| GKVKDLQRDRFARLNASAPSGIAHPALTGDMATLMEAGLLMPLLAALLPILILAPLDKKY | ||
| AHDNHNDILAIYAIFLT | ||
| >N747 | ||
| MGKARGITTAYAYSQVLIGRLGAHAALPYNGSLERKDVAALDAPTNKLYGQFPDGDSWLL | ||
| GALEAYIHTCPPELPQSLATQAPETIFTRLQPYLGLADFGLAHPGQLLKIEATKLQRAVR | ||
| GKFKELQKDAPAQLTANGITVVGQPNLTGDLGTLSEAVVLLQLVPSLLAAIIFKPIDKKY | ||
| GESAPVGILLPFSVW-- | ||
| >N952 | ||
| MGRGRARTTVEAGEKVLLGTMIRFAELPHDGSLQRNDSTALAAPLNTLYAKFPTQDMFLL | ||
| FALESYLHPSSPELGMGLATPAPDILRKRLALFLGLLSFSLEHPIQLLKSLATT-HKAVR | ||
| GPFKDLQKDVPAHLTATAPSGIAHPALTGDMATLMEAVLLMPLLAALLPVLVLKPLDKKF | ||
| ADDSPGDILAVYAIF-- | ||
| >N3964 | ||
| ------RTTVEDNDKVLNATMDRFADLPYDGSLQRDDTTAQTAPLGTLYGKFPTADMFLL | ||
| NALESYLDPKRPELGQGLATKAPDALRKKLQLFLGLLAFALSHPNRLLKSLATT-HKLVR | ||
| GKLKDQEREIFARLTASAPPAIAHPALTGDMATLMEAVLLMPLLAALLTVLPLEPLDKAY | ||
| EDDSPGDILAVYAVF-- | ||
| >N3613 | ||
| LGRGMARTTVEDLETVLNATMDRFAQLPYDGSLQRDDTTAASAPLGTLYGKSPTADMFLQ | ||
| FALESYLDPKRPELGQGLATKAPDALRKRLQLYLGLLSFALEHPTPLLQSLATTLHK-VR | ||
| GKLKNLQREVFARLTASAASGIAHPALTGDMATLMDAVLLMPLLAKLLTIIILEPLDKKY | ||
| SDNSPDDILAAYAAFLS | ||
| >N1689 | ||
| MKLGRYRTVQTANEKYLETTAGRYADQNYAGTAQRGVQKANSVPLGTLYPDLPTRDMLLL | ||
| VSLESYLESITAGL-AGLATKAVTLFKVVLVLFLSVTGFALSHPGELFLSMAAVLQTEIR | ||
| GKLKNLTRELLQKLSASLTAGLAVPELTGDEASLGAGKILVPLLAALLVALLLSPLLGGF | ||
| SDDLPNMVLAIYAVTL- | ||
| >N3700 | ||
| MKMGRPRTKQSTSQRYLDTAGARYDDQAYAGTLQRGLGNAKGVPLGTLYLDFPIRDMLLL | ||
| VTLESYLESIVAGLYA-GATKAPNLLQAVLILFLNVVGFALLHPGALLLTMAAVLHNELI | ||
| GKLKEFSRELLERLAASVITGLAVPELTGDEGTLAAGVILMALLAALLLYLLLDPLLSGF | ||
| SGDLPDSGLAVHA----") |
There was a problem hiding this comment.
Suggested change
| (testpath/"test.fasta").write(">N3289 | |
| --RNRSCRRDNTNGQDLQAALAIFAAKVYVGVALQSVQVAAGIGKHPVYKHIPSKKYTGL | |
| IIQELYLERLMAELADGLADAAPDVLLDIRGLMLALDAPAREKPIIL-LHLAASAGDALR | |
| DKGQALRRELLPRLSGLGYAGLASGALTGDNATLMSARLIGLLVSATLLAL--------- | |
| ----------------- | |
| >N1763 | |
| ------ISKDTTEERFLEVDKLTFAPKSYAGTLQTKILSAVSVPAGTLYKDFPTTELALL | |
| VTLEVYQATDTSGAQDGLAANARDILHVLVELFLALAGFAAQDPLHLLLPMAAALTSSLR | |
| GRLRELRRELLAKGAAKVYTGLGAADATGDGVQLGAASLAMQLLGALLPCLRLDALLGSL | |
| ASGLPEEKLASLAIFL- | |
| >N2100 | |
| --RGRARPKQTTAESNLDATMGKFASQEYDGTMHRELGAASGVSLGTLYPDYPTWEMLIL | |
| VTLESYLEPVVSALYAGLATDAPDILQR-LQLFLALLGFAMNHPGALLKSLAATLESELC | |
| GKLKALTREVLEKLGASVFEGLPEPTLTGDEATPMSAALLMPLVQALLLCLLLQPLLAKH | |
| SDDLPQIILAIYGIF-- | |
| >N774 | |
| --RGRRRTKTIVSEKDLSATMGRFAEQPYDGSLERNAATAASAPLNTMYGEFPTQDMFLL | |
| MCLESYLIPTVLEADAE-ATEARDVLRRRLQLFLALLGFALNHPTQLLKMLATTLHKALR | |
| GKIKDLQREVFARLTASAPAGLAAQFLTGDNATLMEAVLLMPFLAALLSCLILEPLDRKF | |
| ADDFPAVILAIYAIF-- | |
| >N211 | |
| --KARGRTTIETGEKVLTGEMDRFAELQYDGSLQRDDTTGAAPPLGTLYGKLPTQDMFLL | |
| FALESYLDPGTPELGQGLATKAPDGLRKRLHLFLGLLSFSLDHPVHLLKSLATT-HKAVR | |
| GKVKDLQRDRFARLNASAPSGIAHPALTGDMATLMEAGLLMPLLAALLPILILAPLDKKY | |
| AHDNHNDILAIYAIFLT | |
| >N747 | |
| MGKARGITTAYAYSQVLIGRLGAHAALPYNGSLERKDVAALDAPTNKLYGQFPDGDSWLL | |
| GALEAYIHTCPPELPQSLATQAPETIFTRLQPYLGLADFGLAHPGQLLKIEATKLQRAVR | |
| GKFKELQKDAPAQLTANGITVVGQPNLTGDLGTLSEAVVLLQLVPSLLAAIIFKPIDKKY | |
| GESAPVGILLPFSVW-- | |
| >N952 | |
| MGRGRARTTVEAGEKVLLGTMIRFAELPHDGSLQRNDSTALAAPLNTLYAKFPTQDMFLL | |
| FALESYLHPSSPELGMGLATPAPDILRKRLALFLGLLSFSLEHPIQLLKSLATT-HKAVR | |
| GPFKDLQKDVPAHLTATAPSGIAHPALTGDMATLMEAVLLMPLLAALLPVLVLKPLDKKF | |
| ADDSPGDILAVYAIF-- | |
| >N3964 | |
| ------RTTVEDNDKVLNATMDRFADLPYDGSLQRDDTTAQTAPLGTLYGKFPTADMFLL | |
| NALESYLDPKRPELGQGLATKAPDALRKKLQLFLGLLAFALSHPNRLLKSLATT-HKLVR | |
| GKLKDQEREIFARLTASAPPAIAHPALTGDMATLMEAVLLMPLLAALLTVLPLEPLDKAY | |
| EDDSPGDILAVYAVF-- | |
| >N3613 | |
| LGRGMARTTVEDLETVLNATMDRFAQLPYDGSLQRDDTTAASAPLGTLYGKSPTADMFLQ | |
| FALESYLDPKRPELGQGLATKAPDALRKRLQLYLGLLSFALEHPTPLLQSLATTLHK-VR | |
| GKLKNLQREVFARLTASAASGIAHPALTGDMATLMDAVLLMPLLAKLLTIIILEPLDKKY | |
| SDNSPDDILAAYAAFLS | |
| >N1689 | |
| MKLGRYRTVQTANEKYLETTAGRYADQNYAGTAQRGVQKANSVPLGTLYPDLPTRDMLLL | |
| VSLESYLESITAGL-AGLATKAVTLFKVVLVLFLSVTGFALSHPGELFLSMAAVLQTEIR | |
| GKLKNLTRELLQKLSASLTAGLAVPELTGDEASLGAGKILVPLLAALLVALLLSPLLGGF | |
| SDDLPNMVLAIYAVTL- | |
| >N3700 | |
| MKMGRPRTKQSTSQRYLDTAGARYDDQAYAGTLQRGLGNAKGVPLGTLYLDFPIRDMLLL | |
| VTLESYLESIVAGLYA-GATKAPNLLQAVLILFLNVVGFALLHPGALLLTMAAVLHNELI | |
| GKLKEFSRELLERLAASVITGLAVPELTGDEGTLAAGVILMALLAALLLYLLLDPLLSGF | |
| SGDLPDSGLAVHA----") | |
| (testpath/"test.fasta").write <<~EOS | |
| >N3289 | |
| --RNRSCRRDNTNGQDLQAALAIFAAKVYVGVALQSVQVAAGIGKHPVYKHIPSKKYTGL | |
| IIQELYLERLMAELADGLADAAPDVLLDIRGLMLALDAPAREKPIIL-LHLAASAGDALR | |
| DKGQALRRELLPRLSGLGYAGLASGALTGDNATLMSARLIGLLVSATLLAL--------- | |
| ----------------- | |
| >N1763 | |
| ------ISKDTTEERFLEVDKLTFAPKSYAGTLQTKILSAVSVPAGTLYKDFPTTELALL | |
| VTLEVYQATDTSGAQDGLAANARDILHVLVELFLALAGFAAQDPLHLLLPMAAALTSSLR | |
| GRLRELRRELLAKGAAKVYTGLGAADATGDGVQLGAASLAMQLLGALLPCLRLDALLGSL | |
| ASGLPEEKLASLAIFL- | |
| >N2100 | |
| --RGRARPKQTTAESNLDATMGKFASQEYDGTMHRELGAASGVSLGTLYPDYPTWEMLIL | |
| VTLESYLEPVVSALYAGLATDAPDILQR-LQLFLALLGFAMNHPGALLKSLAATLESELC | |
| GKLKALTREVLEKLGASVFEGLPEPTLTGDEATPMSAALLMPLVQALLLCLLLQPLLAKH | |
| SDDLPQIILAIYGIF-- | |
| >N774 | |
| --RGRRRTKTIVSEKDLSATMGRFAEQPYDGSLERNAATAASAPLNTMYGEFPTQDMFLL | |
| MCLESYLIPTVLEADAE-ATEARDVLRRRLQLFLALLGFALNHPTQLLKMLATTLHKALR | |
| GKIKDLQREVFARLTASAPAGLAAQFLTGDNATLMEAVLLMPFLAALLSCLILEPLDRKF | |
| ADDFPAVILAIYAIF-- | |
| >N211 | |
| --KARGRTTIETGEKVLTGEMDRFAELQYDGSLQRDDTTGAAPPLGTLYGKLPTQDMFLL | |
| FALESYLDPGTPELGQGLATKAPDGLRKRLHLFLGLLSFSLDHPVHLLKSLATT-HKAVR | |
| GKVKDLQRDRFARLNASAPSGIAHPALTGDMATLMEAGLLMPLLAALLPILILAPLDKKY | |
| AHDNHNDILAIYAIFLT | |
| >N747 | |
| MGKARGITTAYAYSQVLIGRLGAHAALPYNGSLERKDVAALDAPTNKLYGQFPDGDSWLL | |
| GALEAYIHTCPPELPQSLATQAPETIFTRLQPYLGLADFGLAHPGQLLKIEATKLQRAVR | |
| GKFKELQKDAPAQLTANGITVVGQPNLTGDLGTLSEAVVLLQLVPSLLAAIIFKPIDKKY | |
| GESAPVGILLPFSVW-- | |
| >N952 | |
| MGRGRARTTVEAGEKVLLGTMIRFAELPHDGSLQRNDSTALAAPLNTLYAKFPTQDMFLL | |
| FALESYLHPSSPELGMGLATPAPDILRKRLALFLGLLSFSLEHPIQLLKSLATT-HKAVR | |
| GPFKDLQKDVPAHLTATAPSGIAHPALTGDMATLMEAVLLMPLLAALLPVLVLKPLDKKF | |
| ADDSPGDILAVYAIF-- | |
| >N3964 | |
| ------RTTVEDNDKVLNATMDRFADLPYDGSLQRDDTTAQTAPLGTLYGKFPTADMFLL | |
| NALESYLDPKRPELGQGLATKAPDALRKKLQLFLGLLAFALSHPNRLLKSLATT-HKLVR | |
| GKLKDQEREIFARLTASAPPAIAHPALTGDMATLMEAVLLMPLLAALLTVLPLEPLDKAY | |
| EDDSPGDILAVYAVF-- | |
| >N3613 | |
| LGRGMARTTVEDLETVLNATMDRFAQLPYDGSLQRDDTTAASAPLGTLYGKSPTADMFLQ | |
| FALESYLDPKRPELGQGLATKAPDALRKRLQLYLGLLSFALEHPTPLLQSLATTLHK-VR | |
| GKLKNLQREVFARLTASAASGIAHPALTGDMATLMDAVLLMPLLAKLLTIIILEPLDKKY | |
| SDNSPDDILAAYAAFLS | |
| >N1689 | |
| MKLGRYRTVQTANEKYLETTAGRYADQNYAGTAQRGVQKANSVPLGTLYPDLPTRDMLLL | |
| VSLESYLESITAGL-AGLATKAVTLFKVVLVLFLSVTGFALSHPGELFLSMAAVLQTEIR | |
| GKLKNLTRELLQKLSASLTAGLAVPELTGDEASLGAGKILVPLLAALLVALLLSPLLGGF | |
| SDDLPNMVLAIYAVTL- | |
| >N3700 | |
| MKMGRPRTKQSTSQRYLDTAGARYDDQAYAGTLQRGLGNAKGVPLGTLYLDFPIRDMLLL | |
| VTLESYLESIVAGLYA-GATKAPNLLQAVLILFLNVVGFALLHPGALLLTMAAVLHNELI | |
| GKLKEFSRELLERLAASVITGLAVPELTGDEGTLAAGVILMALLAALLLYLLLDPLLSGF | |
| SGDLPDSGLAVHA----" | |
| EOS |
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HOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source <formula>, where<formula>is the name of the formula you're submitting?brew test <formula>, where<formula>is the name of the formula you're submitting?brew audit --strict <formula>(after doingHOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source <formula>)? If this is a new formula, does it passbrew audit --new <formula>?