diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2023-05-12 22:40:18 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2023-05-12 22:40:18 +0200 |
commit | 662e2e82b1b32b98077ffbf35cf2a6985a2c75e3 (patch) | |
tree | 30b03a7de5a6f6cac6444d7d67898827892a8e54 /gnu/packages/bioinformatics.scm | |
parent | 001d9b1c64dd7274044f4168272146883f34201b (diff) |
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/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 59 |
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 |