diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/gemma.scm | 20 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 2 | ||||
| -rw-r--r-- | gn/packages/phewas.scm | 4 |
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))) |