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-rw-r--r--gn/packages/bioinformatics.scm61
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)