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authorpjotrp2017-12-27 14:06:29 +0000
committerpjotrp2017-12-27 14:06:29 +0000
commitc1de8938169e24114e9d032a52fe6032d5f5f667 (patch)
treec71b337610cb996df0919ead02a4faff6a8c9bbd /gn/packages
parent46d10dff296a1c873a3e7d4f7bc8594de16bee11 (diff)
downloadguix-bioinformatics-c1de8938169e24114e9d032a52fe6032d5f5f667.tar.gz
Added build for faster-lmm-d; moved gsl1
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm71
-rw-r--r--gn/packages/statistics.scm24
2 files changed, 70 insertions, 25 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index aad5b67..82fb121 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -33,6 +33,7 @@
#:use-module (gnu packages gcc)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
+ #:use-module (gnu packages ldc)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
@@ -61,9 +62,53 @@
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
+(define-public faster-lmm-d ; incomplete, just creates builid environment
+ (let ((commit "dea6abf61b633ed55e6a2997068f2d54abe5376b"))
+ (package
+ (name "faster-lmm-d")
+ (version (string-append "0.0.1-" (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjotrp/faster_lmm_d.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1syrn32g1q06bsnrk9wl7q2m5mvvglys2zl92rx0bi49kp2i0ngv"))))
+ (build-system trivial-build-system)
+ (propagated-inputs
+ `(("openblas" ,openblas)
+ ("gsl" ,gsl)
+ ("lapack" ,lapack)
+ ("dub" ,dub)
+ ; ("make" ,make)
+ ))
+ (native-inputs
+ `(("ldc" ,ldc)
+ ("shunit2" ,shunit2)
+ ("which" ,which)
+ ))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let ((target (string-append (assoc-ref %outputs "out")
+ "/share")))
+ (write target)
+ (mkdir-p target)
+ (copy-recursively (assoc-ref %build-inputs "source") target)
+ #t))))
+ (home-page "https://github.com/pjotrp")
+ (synopsis "Parallel LMM")
+ (description
+ ".")
+ (license license:gpl3))))
+
(define-public openblas-haswell
(let ((commit "893bd14e924fa72a4ed345a75d64c637f1b1c550"))
- (package
+ (package
(name "openblas-haswell")
(version (string-append "0.2.20-git-" (string-take commit 7)))
(source (origin
@@ -139,30 +184,6 @@
(license license:bsd-3))))
-(define-public gsl1 ; supporting older GSL tests - no longer really used
- (package
- (name "gsl1")
- (version "1.16")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://gnu/gsl/gsl-"
- version ".tar.gz"))
- (sha256
- (base32
- "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
- ))
- (build-system gnu-build-system)
- (home-page "https://www.gnu.org/software/gsl/")
- (synopsis "Numerical library for C and C++")
- (description
- "The GNU Scientific Library is a library for numerical analysis in C
-and C++. It includes a wide range of mathematical routines, with over 1000
-functions in total. Subject areas covered by the library include:
-differential equations, linear algebra, Fast Fourier Transforms and random
-numbers.")
- (license license:gpl3+)))
-
-
(define-public gemma-gn2 ; guix candidate - generic openblas version
(let ((commit "c760aa09c2aa91ca6270b5f898c27e9aed376a73"))
(package
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index c24c7d0..4159dcd 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -339,3 +339,27 @@ traits (CTL). The additional correlation information obtained can be
combined with QTL information to perform de novo reconstruction of
interaction networks.")
(license license:gpl3)))
+
+
+(define-public gsl1 ; supporting older GSL tests - no longer really used
+ (package
+ (name "gsl1")
+ (version "1.16")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/gsl/gsl-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
+ ))
+ (build-system gnu-build-system)
+ (home-page "https://www.gnu.org/software/gsl/")
+ (synopsis "Numerical library for C and C++")
+ (description
+ "The GNU Scientific Library is a library for numerical analysis in C
+and C++. It includes a wide range of mathematical routines, with over 1000
+functions in total. Subject areas covered by the library include:
+differential equations, linear algebra, Fast Fourier Transforms and random
+numbers.")
+ (license license:gpl3+)))