diff options
| -rw-r--r-- | gn/packages/gemma.scm | 18 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 8 | ||||
| -rw-r--r-- | gn/packages/phewas.scm | 9 |
3 files changed, 18 insertions, 17 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm index 67e8bf7..94433e2 100644 --- a/gn/packages/gemma.scm +++ b/gn/packages/gemma.scm @@ -61,7 +61,6 @@ #:use-module (gn packages shell) #:use-module (srfi srfi-1)) - (define-public gsl (package (name "gsl") @@ -86,30 +85,30 @@ numbers.") (license license:gpl3+))) -(define-public gemma-git ; guix candidate - (let ((commit "c91dfaef84d08ce151eecca50bf8ffdaf4b327f6")) +(define-public gemma-git-gn2 ; guix candidate + (let ((commit "48da44bf2da05f76008b083923ddf5701b9c029a")) (package - (name "gemma-git") - (version (string-append "0.97-pre-" (string-take commit 7))) + (name "gemma-git-gn2") + (version (string-append "0.97-gn2-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/GEMMA") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" version)) (sha256 (base32 - "1ix4p6av88i6jfv84v2qqcmdlnxznp64bm93avrrl68v04jq6psm")))) + "1bvf03aimk1nywv4z8dr75f2qi8mav346w787wzddckakn29yymb")))) (inputs `( ("gsl" ,gsl) ("eigen" ,eigen) + ("shunit2" ,shunit2) ("lapack" ,lapack) ("openblas" ,openblas) ("zlib" ,zlib) )) (native-inputs ; for running tests `(("perl" ,perl) - ("shunit2" ,shunit2) ("which" ,which) )) @@ -121,6 +120,7 @@ numbers.") (assoc-ref %build-inputs "eigen") "/include/eigen3/") "FORCE_DYNAMIC=1" + "DEBUG=1" "WITH_OPENBLAS=1") #:phases ; "/include/eigen3/" @@ -143,7 +143,7 @@ mixed model and some of its close relatives for genome-wide association studies (GWAS).") (license license:gpl3)))) -(define-public gemma +(define-public gemma-gn2 (package (name "gemma") (version "0.96") diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b55c37f..776a7d1 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -44,7 +44,7 @@ #:use-module (gnu packages bootstrap) #:use-module (gnu packages version-control) #:use-module (gn packages bioinformatics) - ; #:use-module (gn packages gemma) + #:use-module (gn packages gemma) #:use-module (gn packages javascript) #:use-module (gn packages phewas) #:use-module (gn packages python) @@ -152,7 +152,7 @@ location of a putative QTL.") (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) (package (name "genenetwork2") - (version (string-append "2.10rc3-" (string-take commit 7) )) + (version (string-append "2.10rc4-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference @@ -175,7 +175,7 @@ location of a putative QTL.") ("r-wgcna" ,r-wgcna) ("redis" ,redis) ("mysql" ,mysql) - ("gemma" ,gemma) + ("gemma-git-gn2" ,gemma-git-gn2) ("genenetwork2-files-small" ,genenetwork2-files-small) ("plink-ng" ,plink-ng) ("pylmm-gn2" ,pylmm-gn2) @@ -233,7 +233,7 @@ location of a putative QTL.") (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) (plink2cmd (string-append (assoc-ref inputs "plink-ng") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + (gemmacmd (string-append (assoc-ref inputs "gemma-git-gn2") "/bin/gemma")) ) (substitute* '("etc/default_settings.py") diff --git a/gn/packages/phewas.scm b/gn/packages/phewas.scm index 2bd832e..59269ef 100644 --- a/gn/packages/phewas.scm +++ b/gn/packages/phewas.scm @@ -19,6 +19,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages cran) #:use-module (gnu packages file) #:use-module (gnu packages gcc) #:use-module (gnu packages java) @@ -117,14 +118,14 @@ genome-wide association studies in structured populations.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.0.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1yq4s4g4xxzcpkv9dpbg29444iy38vfgwj4wgr47rjjq8njfblfx")))) + "1vl9i889800avi8valkl0bz9jrjz71anzmal245ls9gwydrv0dpc")))) (build-system r-build-system) ; (native-inputs ; `(("gfortran" ,gfortran))) @@ -145,14 +146,14 @@ genome-wide association studies in structured populations.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1dijh11v1kr29gnikq09pkdvm3qwmp1a406ahx9l4j6mgn8hlsfq")))) + "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i")))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2) |