diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 61 |
1 files changed, 58 insertions, 3 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 2f588d8..15083f9 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -211,10 +211,64 @@ subsequent visualization, annotation and storage of results.") ;; LGPLv2.1+ (license (list license:gpl2 license:lgpl2.1+)))) -(define-public gemma +(define-public plink-ng + (let ((commit "516d730f9")) + (package + (name "plink-ng") + (version (string-append "1.90b3-" commit )) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chrchang/plink-ng.git") + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf580")) + (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch"))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (zero? (system* "make" "-f" "Makefile.std")) + )) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin/"))) + (install-file "plink2" bin) + #t)))))) + (inputs + `(("zlib" ,zlib) + ("openblas" ,openblas) + ("atlas" ,atlas) + ("lapack" ,lapack) + ("gfortran" ,gfortran) + )) + (native-inputs + `(("unzip" ,unzip))) + (home-page "https://www.cog-genomics.org/plink2") + (synopsis "Whole genome association analysis toolset") + (description + "PLINK is a whole genome association analysis toolset, designed to +perform a range of basic, large-scale analyses in a computationally efficient +manner. The focus of PLINK is purely on analysis of genotype/phenotype data, +so there is no support for steps prior to this (e.g. study design and +planning, generating genotype or CNV calls from raw data). Through +integration with gPLINK and Haploview, there is some support for the +subsequent visualization, annotation and storage of results.") + ;; Code is released under GPLv2, except for fisher.h, which is under + ;; LGPLv2.1+ + (license (list license:gpl2 license:lgpl2.1+))))) + +(define-public gemma-git (let ((commit "2de4bfab3")) (package - (name "gemma") + (name "gemma-git") (version (string-append "0.9.5-" commit )) (source (origin (method git-fetch) @@ -327,7 +381,8 @@ association studies (GWAS).") )) (inputs `( ("mysql" ,mysql) - ("gemma" ,gemma) + ("gemma" ,gemma-git) + ("plink2" ,plink-ng) ("nginx" ,nginx) ("python2-flask" ,python2-flask) ("python2-htmlgen-gn" ,python2-htmlgen-gn) |