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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 70 |
1 files changed, 70 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f0a409d22f..40a0cd24c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1603,6 +1603,76 @@ data and settings.") (license (license:non-copyleft "file://src/COPYING" "See src/COPYING in the distribution.")))) +(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"))) + (mkdir-p bin) + (for-each (lambda (file) + (install-file file bin)) + (find-files "../bin" ".*")) + #t)))))) + (inputs + `(("gsl" ,gsl) + ("lapack" ,lapack) + ("lapack" ,lapack "lapacke") + ("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+)))) + (define-public edirect (package (name "edirect") |