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09/15: gnu: jamm: Use G-expression.
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From: |
guix-commits |
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Subject: |
09/15: gnu: jamm: Use G-expression. |
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Date: |
Fri, 12 May 2023 17:25:44 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit e4ca1bcea53127f4daa358691e46934e70fb908b
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri May 12 22:50:08 2023 +0200
gnu: jamm: Use G-expression.
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
---
gnu/packages/bioinformatics.scm | 77 ++++++++++++++++++++---------------------
1 file changed, 38 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0bdec29807..70134b34e2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15862,46 +15862,45 @@ Barcoding Kit or Rapid Barcoding Kit.")
"0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; there are none
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (delete 'build)
- (replace 'install
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (libexec (string-append out "/libexec/jamm"))
- (bin (string-append out "/bin")))
- (substitute* '("JAMM.sh"
- "SignalGenerator.sh")
- (("^sPath=.*")
- (string-append "sPath=\"" libexec "\"\n")))
- (for-each (lambda (file)
- (install-file file libexec))
- (list "bincalculator.r"
- "peakfinder.r"
- "peakhelper.r"
- "signalmaker.r"
- "xcorr.r"
- "xcorrhelper.r"
- ;; Perl scripts
- "peakfilter.pl"
- "readshifter.pl"))
+ (list
+ #:tests? #f ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda _
+ (let ((libexec (string-append #$output "/libexec/jamm"))
+ (bin (string-append #$output "/bin")))
+ (substitute* '("JAMM.sh"
+ "SignalGenerator.sh")
+ (("^sPath=.*")
+ (string-append "sPath=\"" libexec "\"\n")))
+ (for-each (lambda (file)
+ (install-file file libexec))
+ (list "bincalculator.r"
+ "peakfinder.r"
+ "peakhelper.r"
+ "signalmaker.r"
+ "xcorr.r"
+ "xcorrhelper.r"
+ ;; Perl scripts
+ "peakfilter.pl"
+ "readshifter.pl"))
- (for-each
- (lambda (script)
- (chmod script #o555)
- (install-file script bin)
- (wrap-program (string-append bin "/" script)
- `("PATH" ":" prefix
- (,(string-append (assoc-ref inputs "coreutils") "/bin")
- ,(string-append (assoc-ref inputs "gawk") "/bin")
- ,(string-append (assoc-ref inputs "perl") "/bin")
- ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
- `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
- `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
- (list "JAMM.sh" "SignalGenerator.sh")))
- #t)))))
+ (for-each
+ (lambda (script)
+ (chmod script #o555)
+ (install-file script bin)
+ (wrap-program (string-append bin "/" script)
+ `("PATH" ":" prefix
+ (,(string-append #$(this-package-input "coreutils")
"/bin")
+ ,(string-append #$(this-package-input "gawk") "/bin")
+ ,(string-append #$(this-package-input "perl") "/bin")
+ ,(string-append #$(this-package-input "r-minimal")
"/bin")))
+ `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+ `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+ (list "JAMM.sh" "SignalGenerator.sh"))))))))
(inputs
(list bash
coreutils
- 01/15: gnu: ribotaper: Simplify with G-expression., (continued)
- 01/15: gnu: ribotaper: Simplify with G-expression., guix-commits, 2023/05/12
- 03/15: gnu: methyldackel: Simplify arguments., guix-commits, 2023/05/12
- 02/15: gnu: phast: Simplify by using G-expression., guix-commits, 2023/05/12
- 06/15: gnu: samblaster: Update to 0.1.26., guix-commits, 2023/05/12
- 04/15: gnu: methyldackel: Update to 0.6.1., guix-commits, 2023/05/12
- 07/15: gnu: multichoose: Clean up., guix-commits, 2023/05/12
- 08/15: gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY., guix-commits, 2023/05/12
- 11/15: gnu: python-seaborn: Simplify by using pyproject-build-system., guix-commits, 2023/05/12
- 12/15: gnu: python-pyproject-metadata: Simplify by using pyproject-build-system., guix-commits, 2023/05/12
- 14/15: gnu: python-orjson: Reuse phases from pyproject-build-system., guix-commits, 2023/05/12
- 09/15: gnu: jamm: Use G-expression.,
guix-commits <=
- 10/15: gnu: shrinkwrap: Use pyproject-build-system., guix-commits, 2023/05/12
- 15/15: gnu: python-orjson: Fix version string of Python module., guix-commits, 2023/05/12
- 05/15: gnu: samblaster: Simplify., guix-commits, 2023/05/12
- 13/15: gnu: python-canonicaljson: Use pyproject-build-system., guix-commits, 2023/05/12