From b3394e07071d11674cc796e6a4a3de5fc4634a78 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 14 Aug 2016 02:16:30 -0500
Subject: Getting GN2 ready for new build - plink-ng is disabled and should not
 be built with atlas and lapack (FIXME)

---
 gn/packages/bioinformatics.scm | 14 +++++++-------
 gn/packages/genenetwork.scm    |  9 +++------
 2 files changed, 10 insertions(+), 13 deletions(-)

(limited to 'gn/packages')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c1b22fd..c04c6c8 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -840,8 +840,8 @@ confidence region for the location of a putative QTL.")
     (inputs
      `(("zlib" ,zlib)
        ("openblas" ,openblas)
-       ("atlas" ,atlas)
-       ("lapack" ,lapack)
+       ;; ("atlas" ,atlas)
+       ;; ("lapack" ,lapack)
        ("gfortran" ,gfortran)
        ))
     (native-inputs
@@ -861,7 +861,7 @@ subsequent visualization, annotation and storage of results.")
     (license (list license:gpl2 license:lgpl2.1+))))
 
 (define-public plink-ng
-  (let ((commit "516d730f9"))
+  (let ((commit "6ab6ecf81e904b7db76454422ea59baae437d961"))
   (package
     (name "plink-ng")
     (version (string-append "1.90b3-" commit ))
@@ -873,8 +873,8 @@ subsequent visualization, annotation and storage of results.")
              (file-name (string-append name "-" commit)) 
              (sha256
               (base32
-               "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf580"))
-    (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
+               "0djnfcr3lm6839lkglpq1p4w09zlgv68p618c2i5dng4jhwji94k"))))
+    ;;; (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch"))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ;no "check" target
@@ -894,8 +894,8 @@ subsequent visualization, annotation and storage of results.")
     (inputs
      `(("zlib" ,zlib)
        ("openblas" ,openblas)
-       ("atlas" ,atlas)
-       ("lapack" ,lapack)
+       ;; ("atlas" ,atlas)
+       ;; ("lapack" ,lapack)
        ("gfortran" ,gfortran)
        ))
     (native-inputs
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 4f3d356..10f0a26 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -164,7 +164,7 @@
               ("gemma" ,gemma-git)
               ("genenetwork2-files-small" ,genenetwork2-files-small)
               ("pylmm-gn2" ,pylmm-gn2)
-              ("plink2" ,plink-ng)
+              ;; ("plink2" ,plink-ng) disabled - FIXME
               ("nginx" ,nginx)
               ("python2-flask" ,python2-flask)
               ("python2-htmlgen-gn" ,python2-htmlgen-gn)
@@ -173,7 +173,6 @@
               ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
               ("python2-setuptools" ,python2-setuptools)
               ("python2-scipy" ,python2-scipy)
-              ;; looks like python-numarray is not needed
               ("python2-mysqlclient" ,python2-mysqlclient)
               ("python2-numarray" ,python2-numarray)
               ("python2-numpy" ,python2-numpy)
@@ -189,8 +188,6 @@
               ("python2-simplejson" ,python2-simplejson)
               ("python2-pyyaml" ,python2-pyyaml)
               ("python2-xlsxwriter" ,python2-xlsxwriter)
-              ;; python-yolk is not needed
-              ("plink" ,plink) 
               ("qtlreaper" ,qtlreaper) 
               ))
     (build-system python-build-system)
@@ -203,14 +200,14 @@
                       (let* (
                              (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 "plink2") "/bin/plink2"))
+                             ;; (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2"))
                              (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
                              )
                              
                (substitute* '("etc/default_settings.py")
                             (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
                             (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
-                            (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
+                            ;; (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
                             (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
                             )
                ))))
-- 
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