From 5870720799d5825d1e4a7e6bd7dbf14a99812097 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 9 Jul 2017 11:52:02 +0000
Subject: Update gemma and shunit2 packages

---
 gn/packages/gemma.scm       | 28 +++++++++++++++++++++-------
 gn/packages/genenetwork.scm | 30 +++++++++++++++++++++++++++++-
 gn/packages/shell.scm       | 12 ++++++++++++
 3 files changed, 62 insertions(+), 8 deletions(-)

(limited to 'gn/packages')

diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 3c40317..9986bf5 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -63,28 +63,42 @@
   #:use-module (srfi srfi-1))
 
 (define-public gemma-git ; guix candidate
-  (let ((commit "5675bdf0422f63f81752bb1fcf7b436bc30bf9b7"))
+  (let ((commit "c978835c3630286414df6076d38aad16277cdb6b"))
   (package
     (name "gemma-git")
-    (version (string-append "0.95.2a" commit ))
+    (version (string-append "0.97-" (string-take commit 7)))
     (source (origin
              (method git-fetch)
              (uri (git-reference
-                   (url "https://github.com/xiangzhou/GEMMA")
+                   (url "https://github.com/genenetwork/GEMMA")
                    (commit commit)))
              (file-name (string-append name "-" commit))
              (sha256
               (base32
-               "0qc8dx8m4cqggnin2vsbc9l91ay6h04l0mpjv8z0wcickqb4lby6"))))
+               "1hw8y7vka79v84lv5vyhkinx864yjh1wd8vfd16cvqs1bi8qw3n2"))))
     (inputs `(
               ("gsl" ,gsl)
+              ("eigen" ,eigen)
               ("lapack" ,lapack)
+              ("openblas" ,openblas)
               ("zlib" ,zlib)
               ))
+    (native-inputs ; for running tests
+     `(("shunit2" ,shunit2)
+       ("which" ,which)
+       ))
+
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags '(" FORCE_DYNAMIC=1")
+     `(#:make-flags
+       (list
+        (string-append "EIGEN_INCLUDE_PATH="
+                       (assoc-ref %build-inputs "eigen")
+                       "/include/eigen3/")
+        "FORCE_DYNAMIC=1"
+        "WITH_OPENBLAS=1")
        #:phases
+        ; "/include/eigen3/"
         (modify-phases %standard-phases
          (delete 'configure)
          (add-before 'build 'bin-mkdir
@@ -95,8 +109,8 @@
                   (lambda* (#:key outputs #:allow-other-keys)
                            (let ((out (assoc-ref outputs "out")))
                              (install-file "bin/gemma" (string-append out "/bin"))))))
-       #:tests? #f))
-    (home-page "")
+       #:parallel-tests? #f))
+    (home-page "http://www.xzlab.org/software.html")
     (synopsis "Tool for genome-wide efficient mixed model association")
     (description "GEMMA is the software implementing the Genome-wide
 Efficient Mixed Model Association algorithm for a standard linear
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 08a8954..34178b5 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -91,7 +91,32 @@
     (description #f)
     (license #f)))
 
-(define-public qtlreaper ; guix obsolete - but used in GN2
+(define-public qn-server ; guix obsolete - but used in GN2
+  (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
+  (package
+    (name "qn-server")
+    (version (string-append "1.1-gn2-" (string-take commit 7) ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
+                   (url "https://github.com/pjotrp/QTLreaper.git")
+                   (commit commit)))
+             (file-name (string-append name "-" (string-take commit 7)))
+             (sha256
+              (base32
+               "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test' really!
+    (home-page "")
+    (synopsis "GeneNetwork REST API")
+    (description
+"")
+    (license license:gpl2+))))
+
+(define-public qtlreaper
   (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
   (package
     (name "qtlreaper")
@@ -143,6 +168,7 @@ location of a putative QTL.")
               ("python" ,python-2) ;; probably superfluous
               ("git" ,git)
               ("which" ,which)
+              ("grep" ,grep)
               ("r" ,r)
               ("r-ctl" ,r-ctl)
               ("r-phewas" ,r-phewas)
@@ -198,6 +224,8 @@ location of a putative QTL.")
                             (("echo") (which "echo"))
                             (("redis-server") (which "redis-server"))
                             (("git") (which "git"))
+                            (("grep") (which "grep"))
+                            (("rm") (which "rm"))
                             (("which") (which "which")) ; three wiches in a row!
                             )#t))
            (add-before 'install 'fix-paths
diff --git a/gn/packages/shell.scm b/gn/packages/shell.scm
index e457dce..eb9178f 100644
--- a/gn/packages/shell.scm
+++ b/gn/packages/shell.scm
@@ -3,6 +3,7 @@
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   )
@@ -20,6 +21,9 @@
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32 "11savxc6qliqv25kv59qak6j7syjv95hbpmq1szn1mzn32g2gc25"))))
+    (inputs `(
+              ("coreutils" ,coreutils) ; for mktemp and od
+              ))
       (build-system gnu-build-system)
       (arguments
        `(
@@ -28,6 +32,14 @@
          (modify-phases %standard-phases
            (delete 'configure)
            (delete 'build)
+           (add-after 'unpack 'replace-binary-paths
+                      (lambda _
+                        (substitute* "source/2.0/src/shell/shunit2"
+                                     (("/bin/sh") (which "sh"))
+                                     (("exec mktemp") (string-append "exec " (which "mktemp")))
+                                     (("/usr/bin/od") (which "od"))
+                                     )#t))
+
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
-- 
cgit v1.2.3