From 2c38581c2dcfa3c224f192bfff2c00d87afc8661 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 26 Mar 2018 17:47:21 +0300
Subject: gn: Update genenetwork3 definition

* gn/packages/genenetwork.scm (genenetwork3): Update package
  definition.
  - Deactivate all packages that need Python 2
  - Change the source uri for the package definition
  - Change the commit hash
  - Change the sha256 hash
  - Comment out the processing for pylmmcmd in the 'fix-paths' phase
---
 gn/packages/genenetwork.scm | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 9aa723f..d605dd4 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -396,20 +396,24 @@ location of a putative QTL.")
 
 
 (define-public genenetwork3
-  (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
+  (let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")
+	(commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9"))
     (package
      (name "genenetwork3")
      (version (string-append "2.10rc5-" (string-take commit 7) ))
      (source (origin
 	      (method git-fetch)
 	      (uri (git-reference
-		    (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
+		    (url "https://github.com/fredmanglis/genenetwork2.git")
+		    ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
 		    ;; (url "https://github.com/genenetwork/genenetwork2_diet.git")
 		    (commit commit)))
 	      (file-name (string-append name "-" version))
 	      (sha256
 	       (base32
-		"0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"))))
+		"0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di"
+		;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"
+		))))
      (propagated-inputs ;; propagated for development purposes
       `( ;; Agnostic to Python
 	("r" ,r)
@@ -436,6 +440,7 @@ location of a putative QTL.")
 
 
 	;; With Python3 support
+	("python-wrapper" ,python-wrapper)
 	("gunicorn" ,gunicorn)
 	("python-rpy2" ,python-rpy2)
 	("python-flask" ,python-flask)
@@ -458,12 +463,12 @@ location of a putative QTL.")
 
 
 	;; Without Python3 support
-	("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program
-	("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program
-	("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program
-	("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)
-	("python2-piddle-gn" ,python2-piddle-gn) ;; Run as external python2 program
-	("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions
+	;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program
+	;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program
+	;; ("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program
+	;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)
+	;; ("python2-piddle-gn" ,python2-piddle-gn) ;; Run as external python2 program
+	;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions
 
 
 	;; Removed packages
@@ -500,9 +505,9 @@ location of a putative QTL.")
 		    (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"))
@@ -518,7 +523,7 @@ location of a putative QTL.")
 	       (("^PLINK_COMMAND =.*")
 		(string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
 	       (("^GEMMA_COMMAND =.*")
-		(string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )))))))
+		(string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n")))))))
 	#:tests? #f))   ; no 'setup.py test'
      (home-page "http://genenetwork.org/")
      (synopsis "Full genenetwork services")
-- 
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