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-rw-r--r--gn/packages/gemma.scm20
-rw-r--r--gn/packages/genenetwork.scm2
-rw-r--r--gn/packages/phewas.scm4
3 files changed, 15 insertions, 11 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 82fb121..b2f61a8 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -62,7 +62,7 @@
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
-(define-public faster-lmm-d ; incomplete, just creates builid environment
+(define-public faster-lmm-d ; incomplete, just creates build environment
(let ((commit "dea6abf61b633ed55e6a2997068f2d54abe5376b"))
(package
(name "faster-lmm-d")
@@ -82,6 +82,10 @@
("gsl" ,gsl)
("lapack" ,lapack)
("dub" ,dub)
+ ("gcc" ,gcc)
+ ("glibc" ,glibc)
+ ("binutils" ,binutils) ; for ld linker
+ ("gfortran:lib" ,gfortran "lib")
; ("make" ,make)
))
(native-inputs
@@ -106,10 +110,10 @@
".")
(license license:gpl3))))
-(define-public openblas-haswell
+(define-public openblas-git
(let ((commit "893bd14e924fa72a4ed345a75d64c637f1b1c550"))
(package
- (name "openblas-haswell")
+ (name "openblas-git")
(version (string-append "0.2.20-git-" (string-take commit 7)))
(source (origin
(method git-fetch)
@@ -159,7 +163,7 @@
; ((or (string-prefix? "x86_64" system)
; (string-prefix? "i686" system))
((string-prefix? "x86_64" system)
- '("TARGET=HASWELL"))
+ '("DYNAMIC_ARCH=1"))
;; On MIPS we force the "SICORTEX" TARGET, as for the other
;; two available MIPS targets special extended instructions
;; for Loongson cores are used.
@@ -243,16 +247,16 @@ mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
-(define-public gemma-gn2-haswell ; openblas optimized for haswell
+(define-public gemma-gn2-git ; openblas optimized
(package
(inherit gemma-gn2)
- (name "gemma-gn2-haswell")
+ (name "gemma-gn2-git")
(inputs `(
("gfortran:lib" ,gfortran "lib")
("gsl" ,gsl)
("eigen" ,eigen)
("shunit2" ,shunit2)
- ("openblas" ,openblas-haswell)
+ ("openblas" ,openblas-git)
("zlib" ,zlib)
))
(arguments
@@ -290,7 +294,7 @@ association studies (GWAS).")
(base32
"08apz0imsxzwhzv2iicq2g5zx1iq1vlfrhk7khsfaydshbq5g741"))))
(build-system ruby-build-system)
- (inputs `(("gemma-gn2" ,gemma-gn2-haswell)))
+ (inputs `(("gemma-gn2" ,gemma-gn2-git)))
(arguments
`(#:tests? #f
#:phases
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 479f694..3139599 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -192,7 +192,7 @@ location of a putative QTL.")
("r-wgcna" ,r-wgcna)
("redis" ,redis)
("mysql" ,mysql)
- ("gemma" ,gemma-gn2-haswell)
+ ("gemma" ,gemma-gn2-git)
("gemma-wrapper" ,gemma-wrapper)
("genenetwork2-files-small" ,genenetwork2-files-small)
("plink-ng-gn" ,plink-ng-gn)
diff --git a/gn/packages/phewas.scm b/gn/packages/phewas.scm
index 75d5227..2e91aff 100644
--- a/gn/packages/phewas.scm
+++ b/gn/packages/phewas.scm
@@ -118,14 +118,14 @@ genome-wide association studies in structured populations.")
(define-public r-fgsea
(package
(name "r-fgsea")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fgsea" version))
(sha256
(base32
- "049p2hqsq8iqradqm63ahbn2y6f4y1ys4piz1j6cr00fcfm041jq"))))
+ "187c8xckx0s1p19i85nsiapgb3mppjqxp7zyld5hqyjvw3zcdj50"))))
(build-system r-build-system)
; (native-inputs
; `(("gfortran" ,gfortran)))