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gnu: bamutils: Update to 1.0.14. 

* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
master
Ricardo Wurmus 2021-12-03 13:53:54 +01:00
parent 673cc29908
commit 6d4f260166
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1 changed files with 25 additions and 9 deletions
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@ -324,27 +324,43 @@ BAM files.")
(define-public bamutils (define-public bamutils
(package (package
(name "bamutils") (name "bamutils")
(version "1.0.13") (version "1.0.14")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (uri (git-reference
(string-append (url "https://github.com/statgen/bamUtil")
"https://genome.sph.umich.edu/w/images/7/70/" (commit (string-append "v" version))))
"BamUtilLibStatGen." version ".tgz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0asr1kmjbr3cyf4hkg865y8c2s30v87xvws4q6c8pyfi6wfd1h8n")))) "0i2r332k1kz0jysyg89d858wqq59n16lw6dv5qmilcwshb77r9v7"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; There are no tests. `(#:tests? #f ; Unclear how to run tests
#:make-flags #:make-flags
,#~(list "USER_WARNINGS=-std=gnu++98" ; ,#~(list "USER_WARNINGS=-std=gnu++98" ;
(string-append "INSTALLDIR=" #$output "/bin")) (string-append "INSTALLDIR=" #$output "/bin"))
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure)))) (replace 'configure
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Makefile" ;
(("^DATE=.*") "DATE=\"1970-01-01\"\n"))
(copy-recursively (assoc-ref inputs "libstatgen")
"../libStatGen"))))))
(inputs (inputs
`(("zlib" ,zlib))) `(("zlib" ,zlib)))
(native-inputs
`(("libstatgen"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/statgen/libStatGen/")
(commit (string-append "v" version))))
(file-name (git-file-name "libstatgen" version))
(sha256
(base32
"0q9iyk046r4m7qnav8c3f28zsar25lj9nydiklwaswmzdijhi4p1"))))))
(home-page "https://genome.sph.umich.edu/wiki/BamUtil") (home-page "https://genome.sph.umich.edu/wiki/BamUtil")
(synopsis "Programs for working on SAM/BAM files") (synopsis "Programs for working on SAM/BAM files")
(description "This package provides several programs that perform (description "This package provides several programs that perform