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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
Ricardo Wurmus 2023-05-12 22:40:18 +02:00
parent 001d9b1c64
commit 662e2e82b1
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GPG Key ID: 197A5888235FACAC
1 changed files with 30 additions and 29 deletions
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gnu/packages/bioinformatics.scm
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@ -16525,35 +16525,36 @@ includes a command line tool and an analysis pipeline.")
"0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2")))) "0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; there are none (list
#:tests? #f ;there are none
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
(replace 'configure (replace 'configure
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(let ((htslib (assoc-ref inputs "htslib")))
(substitute* "Makefile" (substitute* "Makefile"
(("-I\\$\\(HTSLIB\\)/htslib") (("-I\\$\\(HTSLIB\\)/htslib")
(string-append "-I" htslib "/include/htslib")) (string-append "-I"
(search-input-directory inputs "/include/htslib")))
((" \\$\\(HTSLIB\\)/libhts.a") ((" \\$\\(HTSLIB\\)/libhts.a")
(string-append " " htslib "/lib/libhts.so")))) (string-append " " (search-input-file inputs "/lib/libhts.so"))))
(let ((samtools (search-input-file inputs "/bin/samtools")))
(substitute* "run_arriba.sh" (substitute* "run_arriba.sh"
(("^STAR ") (string-append (which "STAR") " ")) (("^STAR ")
(string-append (search-input-file inputs "/bin/STAR") " "))
(("samtools --version-only") (("samtools --version-only")
(string-append (which "samtools") " --version-only")) (string-append samtools " --version-only"))
(("samtools index") (("samtools index")
(string-append (which "samtools") " index")) (string-append samtools " index"))
(("samtools sort") (("samtools sort")
(string-append (which "samtools") " sort"))) (string-append samtools " sort"))))))
#t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda _
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (let ((bin (string-append #$output "/bin")))
(install-file "arriba" bin) (install-file "arriba" bin)
(install-file "run_arriba.sh" bin) (install-file "run_arriba.sh" bin)
(install-file "draw_fusions.R" bin) (install-file "draw_fusions.R" bin)
(wrap-program (string-append bin "/draw_fusions.R") (wrap-program (string-append bin "/draw_fusions.R")
`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))))))))
#t)))))
(inputs (inputs
(list htslib (list htslib
r-minimal r-minimal