gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY.
* gnu/packages/bioinformatics.scm (arriba)[arguments]: Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop trailing #T from build phases.master
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@ -16525,35 +16525,36 @@ includes a command line tool and an analysis pipeline.")
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"0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2"))))
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"0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2"))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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`(#:tests? #f ; there are none
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(list
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#:phases
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#:tests? #f ;there are none
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(modify-phases %standard-phases
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#:phases
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(replace 'configure
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#~(modify-phases %standard-phases
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(lambda* (#:key inputs #:allow-other-keys)
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(replace 'configure
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(let ((htslib (assoc-ref inputs "htslib")))
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "Makefile"
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(substitute* "Makefile"
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(("-I\\$\\(HTSLIB\\)/htslib")
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(("-I\\$\\(HTSLIB\\)/htslib")
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(string-append "-I" htslib "/include/htslib"))
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(string-append "-I"
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((" \\$\\(HTSLIB\\)/libhts.a")
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(search-input-directory inputs "/include/htslib")))
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(string-append " " htslib "/lib/libhts.so"))))
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((" \\$\\(HTSLIB\\)/libhts.a")
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(substitute* "run_arriba.sh"
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(string-append " " (search-input-file inputs "/lib/libhts.so"))))
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(("^STAR ") (string-append (which "STAR") " "))
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(let ((samtools (search-input-file inputs "/bin/samtools")))
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(("samtools --version-only")
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(substitute* "run_arriba.sh"
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(string-append (which "samtools") " --version-only"))
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(("^STAR ")
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(("samtools index")
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(string-append (search-input-file inputs "/bin/STAR") " "))
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(string-append (which "samtools") " index"))
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(("samtools --version-only")
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(("samtools sort")
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(string-append samtools " --version-only"))
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(string-append (which "samtools") " sort")))
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(("samtools index")
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#t))
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(string-append samtools " index"))
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(replace 'install
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(("samtools sort")
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(lambda* (#:key outputs #:allow-other-keys)
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(string-append samtools " sort"))))))
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(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
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(replace 'install
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(install-file "arriba" bin)
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(lambda _
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(install-file "run_arriba.sh" bin)
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(let ((bin (string-append #$output "/bin")))
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(install-file "draw_fusions.R" bin)
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(install-file "arriba" bin)
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(wrap-program (string-append bin "/draw_fusions.R")
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(install-file "run_arriba.sh" bin)
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`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
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(install-file "draw_fusions.R" bin)
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#t)))))
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(wrap-program (string-append bin "/draw_fusions.R")
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`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))))))))
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(inputs
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(inputs
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(list htslib
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(list htslib
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r-minimal
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r-minimal
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