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branch master updated: gnu: kaiju: Update to 1.9.0.
From: |
guix-commits |
Subject: |
branch master updated: gnu: kaiju: Update to 1.9.0. |
Date: |
Tue, 04 Oct 2022 17:13:18 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 9ed65e6af7 gnu: kaiju: Update to 1.9.0.
9ed65e6af7 is described below
commit 9ed65e6af77893b658a7159b091b5002892c2f95
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Oct 4 23:07:19 2022 +0200
gnu: kaiju: Update to 1.9.0.
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0.
[arguments]: Use gexps; wrap scripts in install phase.
[inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip,
python-wrapper, tar, and wget.
---
gnu/packages/bioinformatics.scm | 53 ++++++++++++++++++++++++++++-------------
1 file changed, 37 insertions(+), 16 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 249b956c88..0404253193 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4845,7 +4845,7 @@ data.")
(define-public kaiju
(package
(name "kaiju")
- (version "1.6.3")
+ (version "1.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -4854,24 +4854,45 @@ data.")
(file-name (git-file-name name version))
(sha256
(base32
- "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x"))))
+ "1hfmadkfs6jjd7l3byly5xxb0ifm3dm1wis11sjbqfcv6l89snmg"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; There are no tests.
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (add-before 'build 'move-to-src-dir
- (lambda _ (chdir "src") #t))
- (replace 'install
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (mkdir-p bin)
- (chdir "..")
- (copy-recursively "bin" bin))
- #t)))))
+ (list
+ #:tests? #f ; There are no tests.
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'move-to-src-dir
+ (lambda _ (chdir "src")))
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append #$output "/bin")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin)
+ (let ((path (search-path-as-list '("bin")
+ '#$(match (package-inputs
this-package)
+ (((_ pkg) ...) pkg)))))
+ (for-each (lambda (script)
+ (let ((exe (string-append bin "/" script)))
+ (chmod exe #o555)
+ (wrap-script exe
+ #:guile #$(file-append guile-3.0
"/bin/guile")
+ `("PATH" ":" prefix ,path))))
+ (list "kaiju-convertMAR.py"
+ "kaiju-gbk2faa.pl"
+ "kaiju-makedb")))))))))
(inputs
- (list perl zlib))
+ (list bzip2
+ coreutils
+ curl
+ gawk
+ guile-3.0 ;for wrap-script
+ gzip
+ perl
+ python-wrapper
+ tar
+ wget
+ zlib))
(home-page "http://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification
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