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gnu: eigensoft: Update to 7.2.1. 

* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
This commit is contained in:
Ricardo Wurmus 2018-10-21 20:58:45 +02:00
parent 5748fe5fcc
commit 949fa34b84
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1 changed files with 52 additions and 61 deletions
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@ -2274,72 +2274,63 @@ of nucleic acid binding proteins.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public eigensoft (define-public eigensoft
(let ((revision "1") (package
(commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) (name "eigensoft")
(package (version "7.2.1")
(name "eigensoft") (source
(version (string-append "6.1.2-" (origin
revision "." (method git-fetch)
(string-take commit 9))) (uri (git-reference
(source (url "https://github.com/DReichLab/EIG.git")
(origin (commit (string-append "v" version))))
(method git-fetch) (file-name (git-file-name name version))
(uri (git-reference (sha256
(url "https://github.com/DReichLab/EIG.git") (base32
(commit commit))) "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k"))
(file-name (string-append "eigensoft-" commit "-checkout")) (modules '((guix build utils)))
(sha256 ;; Remove pre-built binaries.
(base32 (snippet '(begin
"0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) (delete-file-recursively "bin")
(modules '((guix build utils))) (mkdir "bin")
;; Remove pre-built binaries. #t))))
(snippet '(begin (build-system gnu-build-system)
(delete-file-recursively "bin") (arguments
(mkdir "bin") `(#:tests? #f ; There are no tests.
#t)))) #:make-flags '("CC=gcc")
(build-system gnu-build-system) #:phases
(arguments (modify-phases %standard-phases
`(#:tests? #f ; There are no tests. ;; There is no configure phase, but the Makefile is in a
#:make-flags '("CC=gcc") ;; sub-directory.
#:phases (replace 'configure
(modify-phases %standard-phases (lambda _ (chdir "src") #t))
;; There is no configure phase, but the Makefile is in a ;; The provided install target only copies executables to
;; sub-directory. ;; the "bin" directory in the build root.
(replace 'configure (add-after 'install 'actually-install
(lambda _ (lambda* (#:key outputs #:allow-other-keys)
(chdir "src") (let* ((out (assoc-ref outputs "out"))
;; The link flags are incomplete. (bin (string-append out "/bin")))
(substitute* "Makefile" (for-each (lambda (file)
(("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) (install-file file bin))
#t)) (find-files "../bin" ".*"))
;; The provided install target only copies executables to #t))))))
;; the "bin" directory in the build root. (inputs
(add-after 'install 'actually-install `(("gsl" ,gsl)
(lambda* (#:key outputs #:allow-other-keys) ("lapack" ,lapack)
(let* ((out (assoc-ref outputs "out")) ("openblas" ,openblas)
(bin (string-append out "/bin"))) ("perl" ,perl)
(for-each (lambda (file) ("gfortran" ,gfortran "lib")))
(install-file file bin)) (home-page "https://github.com/DReichLab/EIG")
(find-files "../bin" ".*")) (synopsis "Tools for population genetics")
#t)))))) (description "The EIGENSOFT package provides tools for population
(inputs
`(("gsl" ,gsl)
("lapack" ,lapack)
("openblas" ,openblas)
("perl" ,perl)
("gfortran" ,gfortran "lib")))
(home-page "https://github.com/DReichLab/EIG")
(synopsis "Tools for population genetics")
(description "The EIGENSOFT package provides tools for population
genetics and stratification correction. EIGENSOFT implements methods commonly genetics and stratification correction. EIGENSOFT implements methods commonly
used in population genetics analyses such as PCA, computation of Tracy-Widom used in population genetics analyses such as PCA, computation of Tracy-Widom
statistics, and finding related individuals in structured populations. It statistics, and finding related individuals in structured populations. It
comes with a built-in plotting script and supports multiple file formats and comes with a built-in plotting script and supports multiple file formats and
quantitative phenotypes.") quantitative phenotypes.")
;; The license of the eigensoft tools is Expat, but since it's ;; The license of the eigensoft tools is Expat, but since it's
;; linking with the GNU Scientific Library (GSL) the effective ;; linking with the GNU Scientific Library (GSL) the effective
;; license is the GPL. ;; license is the GPL.
(license license:gpl3+)))) (license license:gpl3+)))
(define-public edirect (define-public edirect
(package (package