From e472db7bd929f8b511b0cd5e777dff25c1fbc692 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 20 Feb 2016 13:03:51 +0000
Subject: Added package for pylmm

---
 gn/packages/statistics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gn')

diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index 065826e..c10ba29 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -148,3 +148,27 @@
      "R/lmmlite")
     (home-page "https://github.com/kbroman/")
     (license license:asl2.0)))
+
+(define-public pylmm-gn2
+  (let ((commit "f5c9e2378"))
+  (package
+    (name "pylmm-gn2")
+    (version (string-append "1.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/genenetwork/pylmm.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "10qb5dpwqjdiq9gakl7m4p4ckjlc701mzqpgbhp89w1aysddj1c7"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test'
+    (home-page "http://genenetwork.org/")
+    (synopsis "LMM resolver")
+    (description "Fast and lightweight linear mixed-model (LMM) solver
+for use in genome-wide association studies (GWAS).")
+    (license license:agpl3+))))
-- 
cgit v1.2.3


From dd74ba8cd335ac94dca916549a2b9edbc0332748 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 20 Feb 2016 13:07:43 +0000
Subject: Adding pylmm to gn2

---
 gn/packages/bioinformatics.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1aee0ef..0d3a765 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -44,6 +44,7 @@
   #:use-module (gnu packages zip)
   #:use-module (gnu packages bootstrap)
   #:use-module (gn packages python)
+  #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
 (define-public my-deploy
@@ -380,6 +381,7 @@ association studies (GWAS).")
     (inputs `(
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
+              ("pylmm-gn2" ,pylmm-gn2)
               ("plink2" ,plink-ng)
               ("nginx" ,nginx)
               ("python2-flask" ,python2-flask)
-- 
cgit v1.2.3


From dfb685956526dce67a8e03849bffd1d9d52c5958 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 20 Feb 2016 14:18:45 +0000
Subject: pylmm: Patch wrapper script so it points to the correct locations.

---
 gn/packages/statistics.scm | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index c10ba29..2d83816 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -150,7 +150,7 @@
     (license license:asl2.0)))
 
 (define-public pylmm-gn2
-  (let ((commit "f5c9e2378"))
+  (let ((commit "3c6d1cac8"))
   (package
     (name "pylmm-gn2")
     (version (string-append "1.0-" commit ))
@@ -162,11 +162,27 @@
              (file-name (string-append name "-" commit)) 
              (sha256
               (base32
-               "10qb5dpwqjdiq9gakl7m4p4ckjlc701mzqpgbhp89w1aysddj1c7"))))
+               "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964"))))
     (build-system python-build-system)
+    (inputs `(
+              ("python2-setuptools" ,python2-setuptools)
+              ("python2-scipy" ,python2-scipy)
+              ("python2-numpy" ,python2-numpy)
+              ))
     (arguments
      `(#:python ,python-2
-       #:tests? #f))   ; no 'setup.py test'
+       #:tests? #f        ; no 'setup.py test'
+       #:phases
+       (modify-phases %standard-phases
+         (add-before
+          'build 'change-paths
+          (lambda* (#:key outputs #:allow-other-keys)
+                   (let ((out (assoc-ref outputs "out")))
+                     (substitute* "scripts/pylmm_redis"
+                                  (("/usr/bin/python") (which "python"))
+                                  (("\\$PACKAGEDIR") (string-append out "/lib/python2.7/site-packages")))
+                     ))))))
+
     (home-page "http://genenetwork.org/")
     (synopsis "LMM resolver")
     (description "Fast and lightweight linear mixed-model (LMM) solver
-- 
cgit v1.2.3