gnu: python-pysam: Delete bundled htslib.
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet to delete htslib. [arguments]: Add htslib flags in 'set-flags phase. [propagated-inputs]: New field. Add htslib.
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@ -1354,17 +1354,28 @@ multiple sequence alignments.")
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(uri (pypi-uri "pysam" version))
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(sha256
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(base32
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"1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn"))))
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"1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn"))
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(modules '((guix build utils)))
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(snippet
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;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
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'(delete-file-recursively "htslib"))))
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(build-system python-build-system)
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(arguments
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`(#:tests? #f ; tests are excluded in the manifest
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#:phases
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(modify-phases %standard-phases
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(add-before 'build 'set-flags
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(lambda _
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "HTSLIB_MODE" "external")
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(setenv "HTSLIB_LIBRARY_DIR"
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(string-append (assoc-ref inputs "htslib") "/lib"))
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(setenv "HTSLIB_INCLUDE_DIR"
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(string-append (assoc-ref inputs "htslib") "/include"))
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(setenv "LDFLAGS" "-lncurses")
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(setenv "CFLAGS" "-D_CURSES_LIB=1")
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#t)))))
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(propagated-inputs
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`(("htslib" ,htslib))) ; Included from installed header files.
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(inputs
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`(("ncurses" ,ncurses)
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("zlib" ,zlib)))
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