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01/11: gnu: samtools: Use "modify-phases" syntax.
From: |
Ben Woodcroft |
Subject: |
01/11: gnu: samtools: Use "modify-phases" syntax. |
Date: |
Sat, 22 Jul 2017 20:31:59 -0400 (EDT) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit c842d425933d0b7d6c5e88bb5fd52c3008b8951d
Author: Ben Woodcroft <address@hidden>
Date: Thu Apr 6 22:27:23 2017 +1000
gnu: samtools: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
---
gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++----------------------
1 file changed, 19 insertions(+), 22 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 16339f9..7669b4c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4533,29 +4533,26 @@ to the user's query of interest.")
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
#:configure-flags (list "--with-ncurses")
#:phases
- (alist-cons-after
- 'unpack 'patch-tests
- (lambda _
- (substitute* "test/test.pl"
- ;; The test script calls out to /bin/bash
- (("/bin/bash") (which "bash")))
- #t)
- (alist-cons-after
- 'install 'install-library
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
- (install-file "libbam.a" lib)
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-tests
+ (lambda _
+ (substitute* "test/test.pl"
+ ;; The test script calls out to /bin/bash
+ (("/bin/bash") (which "bash")))
#t))
- (alist-cons-after
- 'install 'install-headers
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((include (string-append (assoc-ref outputs "out")
- "/include/samtools/")))
- (for-each (lambda (file)
- (install-file file include))
- (scandir "." (lambda (name) (string-match "\\.h$"
name))))
- #t))
- %standard-phases)))))
+ (add-after 'install 'install-library
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+ (install-file "libbam.a" lib)
+ #t)))
+ (add-after 'install 'install-headers
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((include (string-append (assoc-ref outputs "out")
+ "/include/samtools/")))
+ (for-each (lambda (file)
+ (install-file file include))
+ (scandir "." (lambda (name) (string-match "\\.h$"
name))))
+ #t))))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses)
("perl" ,perl)
- branch master updated (c62d1a6 -> f3f68a4), Ben Woodcroft, 2017/07/22
- 03/11: gnu: samtools: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 06/11: gnu: python-pysam: Update to 0.11.2.2., Ben Woodcroft, 2017/07/22
- 01/11: gnu: samtools: Use "modify-phases" syntax.,
Ben Woodcroft <=
- 02/11: gnu: htslib: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 05/11: gnu: bamm: Use htslib-1.3., Ben Woodcroft, 2017/07/22
- 07/11: gnu: htslib: Update to 1.5., Ben Woodcroft, 2017/07/22
- 09/11: gnu: bcftools: Update to 1.5., Ben Woodcroft, 2017/07/22
- 04/11: gnu: bcftools: Update to 1.4.1., Ben Woodcroft, 2017/07/22
- 08/11: gnu: samtools: Update to 1.5., Ben Woodcroft, 2017/07/22
- 11/11: gnu: metabat: Update to 2.11.1., Ben Woodcroft, 2017/07/22
- 10/11: gnu: python-plastid: Update to 0.4.8., Ben Woodcroft, 2017/07/22