diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 113 |
1 files changed, 52 insertions, 61 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b6bd2c619a..d0f4429a4c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2274,72 +2274,63 @@ of nucleic acid binding proteins.") (license license:gpl3+))) (define-public eigensoft - (let ((revision "1") - (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) - (package - (name "eigensoft") - (version (string-append "6.1.2-" - revision "." - (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DReichLab/EIG.git") - (commit commit))) - (file-name (string-append "eigensoft-" commit "-checkout")) - (sha256 - (base32 - "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) - (modules '((guix build utils))) - ;; Remove pre-built binaries. - (snippet '(begin - (delete-file-recursively "bin") - (mkdir "bin") - #t)))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:make-flags '("CC=gcc") - #:phases - (modify-phases %standard-phases - ;; There is no configure phase, but the Makefile is in a - ;; sub-directory. - (replace 'configure - (lambda _ - (chdir "src") - ;; The link flags are incomplete. - (substitute* "Makefile" - (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) - #t)) - ;; The provided install target only copies executables to - ;; the "bin" directory in the build root. - (add-after 'install 'actually-install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "../bin" ".*")) - #t)))))) - (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 + (package + (name "eigensoft") + (version "7.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DReichLab/EIG.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k")) + (modules '((guix build utils))) + ;; Remove pre-built binaries. + (snippet '(begin + (delete-file-recursively "bin") + (mkdir "bin") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + ;; There is no configure phase, but the Makefile is in a + ;; sub-directory. + (replace 'configure + (lambda _ (chdir "src") #t)) + ;; The provided install target only copies executables to + ;; the "bin" directory in the build root. + (add-after 'install 'actually-install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "../bin" ".*")) + #t)))))) + (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 used in population genetics analyses such as PCA, computation of Tracy-Widom statistics, and finding related individuals in structured populations. It comes with a built-in plotting script and supports multiple file formats and quantitative phenotypes.") - ;; The license of the eigensoft tools is Expat, but since it's - ;; linking with the GNU Scientific Library (GSL) the effective - ;; license is the GPL. - (license license:gpl3+)))) + ;; The license of the eigensoft tools is Expat, but since it's + ;; linking with the GNU Scientific Library (GSL) the effective + ;; license is the GPL. + (license license:gpl3+))) (define-public edirect (package |