From aea8bc0de6a1fce08a0f0adbc5b2a295264ff550 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 6 Sep 2019 02:40:12 -0500
Subject: Cleaning up genenetwork2 build.

Remove pylmm and r-phewas. Added rust-qtlreaper
Fixed python-setuptools warning
---
 gn/packages/cwl.scm         | 2 +-
 gn/packages/genenetwork.scm | 9 +++++----
 gn/packages/python.scm      | 4 ++--
 3 files changed, 8 insertions(+), 7 deletions(-)

(limited to 'gn/packages')

diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 84251a4..dddaa8a 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -13,7 +13,7 @@
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages time)
   #:use-module (gnu packages version-control)
-  #:use-module (gn packages python)
+  ; #:use-module (gn packages python)
   #:use-module (guix download)
   #:use-module (guix packages)
   #:use-module (guix git-download)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 27eb154..46e0407 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -31,7 +31,7 @@
   #:use-module (gn packages gemma)
   #:use-module (gn packages javascript)
   #:use-module (gn packages phewas)
-  #:use-module (gn packages python)
+  #:use-module (gn packages python) 
   #:use-module (gn packages python24)
   #:use-module (gn packages statistics))
 
@@ -237,7 +237,7 @@ location of a putative QTL.")
        ("grep" ,grep)
        ("r" ,r)
        ("r-ctl" ,r-ctl)
-       ("r-phewas" ,r-phewas)
+       ; ("r-phewas" ,r-phewas)
        ("r-qtl" ,r-qtl)
        ("r-wgcna" ,r-wgcna)
        ("redis" ,redis)
@@ -246,7 +246,8 @@ location of a putative QTL.")
        ("gemma-wrapper" ,gemma-wrapper)
        ; ("genenetwork2-files-small" ,genenetwork2-files-small)
        ("plink-ng-gn" ,plink-ng-gn)
-       ("pylmm-gn2" ,pylmm-gn2)
+       ; ("pylmm-gn2" ,pylmm-gn2)
+       ("rust-qtlreaper" ,rust-qtlreaper)
        ("nginx" ,nginx)
        ("python2-flask" ,python2-flask)
        ("gunicorn" ,gunicorn)
@@ -310,7 +311,7 @@ location of a putative QTL.")
              (lambda* (#:key inputs #:allow-other-keys)
                (let* (
                       ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2"))
-                      (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
+                      ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
                       (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
                       (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
                       )
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index b393ebb..3c03e26 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -412,9 +412,9 @@ until a value is returned.")
 (define-public python2-rserve
   (package-with-python2 python-rserve))
 
-(define-public python-setuptools
+(define-public python-setuptools-old
   (package
-    (name "python-setuptools")
+    (name "python-setuptools-old")
     (version "40.6.0")
     (source
      (origin
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