From a4a9f2eec7a770a52bbeda64169ba9e3b1ff2583 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 5 Mar 2016 16:07:32 +0000
Subject: Guix paths to the tools

---
 gn/packages/bioinformatics.scm |  2 +-
 gn/packages/genenetwork.scm    | 20 +++++++++++++++++---
 gn/packages/python.scm         |  2 ++
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 295a2b3..c04c928 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -305,8 +305,8 @@ length of a short-read sequencing alignment.")
   (propagated-inputs
    `( ;; ("r-annotationdbi" ,r-annotationdbi)
      ; ("r-biocparallel" ,r-biocparallel)
-     ("r-dynamictreecut" ,r-dynamictreecut)
      ("r-doparallel" ,r-doparallel)
+     ("r-dynamictreecut" ,r-dynamictreecut)
      ("r-fastcluster" ,r-fastcluster)
      ("r-foreach" ,r-foreach)
      ("r-go-db" ,r-go-db)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index fdcbb7f..c952792 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -154,10 +154,14 @@
              (sha256
               (base32
                "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
+    (inputs `(
+              ("r-wgcna" ,r-wgcna)
+              ("r-qtl" ,r-qtl)))
     (propagated-inputs `(  ;; propagated for development purposes
               ("python" ,python-2) ;; probably superfluous
               ("r" ,r)
               ("r-wgcna" ,r-wgcna)
+              ("r-qtl" ,r-qtl)
               ("redis" ,redis)
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
@@ -190,7 +194,6 @@
               ;; python-yolk is not needed
               ("plink" ,plink) 
               ("qtlreaper" ,qtlreaper) 
-              ("r-qtl" ,r-qtl)
               ))
     (build-system python-build-system)
     (arguments
@@ -199,9 +202,20 @@
          (modify-phases %standard-phases
            (add-before 'install 'fix-paths
              (lambda* (#:key inputs #:allow-other-keys)
-               (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )))
+                      (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"))
+                             (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+                             )
+                             
                (substitute* '("etc/default_settings.py")
-                 (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )))))))
+                            (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
+                            (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
+                            (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
+                            (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
+                            )
+               ))))
        #:tests? #f))   ; no 'setup.py test'
     (home-page "http://genenetwork.org/")
     (synopsis "Full genenetwork services")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 6fff9a3..8157c0b 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -432,6 +432,8 @@ version ".tgz"))
     (build-system python-build-system)
     (native-inputs
      `(("python2-setuptools" ,python2-setuptools)))
+    (propagated-inputs
+     `(("python2-pil" ,python2-pil)))
     (arguments
      `(
        #:python ,python-2
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