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authorRicardo Wurmus <rekado@elephly.net>2023-05-12 22:40:18 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-05-12 22:40:18 +0200
commit662e2e82b1b32b98077ffbf35cf2a6985a2c75e3 (patch)
tree30b03a7de5a6f6cac6444d7d67898827892a8e54 /gnu
parent001d9b1c64dd7274044f4168272146883f34201b (diff)
downloadguix-662e2e82b1b32b98077ffbf35cf2a6985a2c75e3.tar
guix-662e2e82b1b32b98077ffbf35cf2a6985a2c75e3.tar.gz
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.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm59
1 files changed, 30 insertions, 29 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6d34c0abab..0bdec29807 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16525,35 +16525,36 @@ includes a command line tool and an analysis pipeline.")
"0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; there are none
- #:phases
- (modify-phases %standard-phases
- (replace 'configure
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((htslib (assoc-ref inputs "htslib")))
- (substitute* "Makefile"
- (("-I\\$\\(HTSLIB\\)/htslib")
- (string-append "-I" htslib "/include/htslib"))
- ((" \\$\\(HTSLIB\\)/libhts.a")
- (string-append " " htslib "/lib/libhts.so"))))
- (substitute* "run_arriba.sh"
- (("^STAR ") (string-append (which "STAR") " "))
- (("samtools --version-only")
- (string-append (which "samtools") " --version-only"))
- (("samtools index")
- (string-append (which "samtools") " index"))
- (("samtools sort")
- (string-append (which "samtools") " sort")))
- #t))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "arriba" bin)
- (install-file "run_arriba.sh" bin)
- (install-file "draw_fusions.R" bin)
- (wrap-program (string-append bin "/draw_fusions.R")
- `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
- #t)))))
+ (list
+ #:tests? #f ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("-I\\$\\(HTSLIB\\)/htslib")
+ (string-append "-I"
+ (search-input-directory inputs "/include/htslib")))
+ ((" \\$\\(HTSLIB\\)/libhts.a")
+ (string-append " " (search-input-file inputs "/lib/libhts.so"))))
+ (let ((samtools (search-input-file inputs "/bin/samtools")))
+ (substitute* "run_arriba.sh"
+ (("^STAR ")
+ (string-append (search-input-file inputs "/bin/STAR") " "))
+ (("samtools --version-only")
+ (string-append samtools " --version-only"))
+ (("samtools index")
+ (string-append samtools " index"))
+ (("samtools sort")
+ (string-append samtools " sort"))))))
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append #$output "/bin")))
+ (install-file "arriba" bin)
+ (install-file "run_arriba.sh" bin)
+ (install-file "draw_fusions.R" bin)
+ (wrap-program (string-append bin "/draw_fusions.R")
+ `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))))))))
(inputs
(list htslib
r-minimal