Conflict

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)