gn-guile: Modify phases to fix load paths.

1 files changed, 64 insertions, 5 deletions

diff --git a/guix/gn-machines/genenetwork.scm b/guix/gn-machines/genenetwork.scm
index d976e27..8dd968d 100644
--- a/guix/gn-machines/genenetwork.scm
+++ b/guix/gn-machines/genenetwork.scm
@@ -1,14 +1,17 @@
 (define-module (gn-machines genenetwork)
+  #:use-module (guix)
+  #:use-module (guix packages)
+  #:use-module (guix git-download)
+
+  #:use-module ((gnu packages ssh) #:select (openssh-sans-x))
+  #:use-module ((gnu packages guile-xyz) #:select (guile-config))
+
   #:use-module ((gn packages genenetwork)
                 #:select (genenetwork2 genenetwork3 gn-auth gn-uploader gn-libs)
                 #:prefix gn:)
   #:use-module((gn packages guile)
                #:select (gn-guile guile-sheepdog)
-               #:prefix gng:)
-  #:use-module (guix git-download)
-  #:use-module (guix packages)
-  #:use-module ((gnu packages ssh) #:select (openssh-sans-x))
-  #:use-module ((gnu packages guile-xyz) #:select (guile-config)))
+               #:prefix gng:))
 
 (define-public genenetwork2
   (let ((commit "ef4776ea476d3276f4297e39694a16712978653c")
@@ -128,6 +131,62 @@
 		(sha256
 		 (base32
                   "0ylv4psdmd442jg73sw8danv9n9wj3wi8b96jfnzx025llz9ka3m"))))
+      (arguments
+       (list
+	#:not-compiled-file-regexp "(guix|guix/.*)[.]scm$"
+	#:modules '((srfi srfi-1)
+		    (guix build guile-build-system)
+		    (guix build utils))
+	#:phases
+	#~(modify-phases %standard-phases
+	    (add-after 'unpack 'patch-git
+	      (lambda* (#:key inputs #:allow-other-keys)
+	        (let ((git (search-input-file inputs "/bin/git")))
+	          (substitute* "web/view/markdown.scm"
+	            (("\"git\"") (string-append "\"" git "\""))
+	            (("git -C") (string-append git " -C")))
+                  (substitute* "gn-guile.sh"
+                    ((" @SHELL@")
+                     (search-input-file inputs "/bin/bash"))
+	            (("guile") (search-input-file inputs "/bin/guile"))
+                    (("main web")
+                     (string-append "main " #$output
+                                    "/share/guile/site/"
+                                    (target-guile-effective-version)
+                                    "/web"))))))
+            (add-after 'build 'install-scripts
+              (lambda* _
+                (mkdir-p "bin")
+		(copy-file "gn-guile.sh" "bin/gn-guile")
+		(copy-file "scripts/lmdb-publishdata-export.scm"
+			   "bin/lmdb-publishdata-export")
+                (for-each (lambda (script-path)
+                            (install-file script-path
+                                          (string-append #$output "/bin")))
+                          (list "bin/gn-guile"
+                                "bin/lmdb-publishdata-export"))))
+            (add-after 'install-scripts 'wrap
+              (lambda* (#:key inputs #:allow-other-keys)
+                (let((effective-version (target-guile-effective-version))
+                     (guile-path
+                      (dirname (search-input-file inputs "/bin/guile"))))
+                  (for-each (lambda (script-name)
+                              (wrap-program
+                                  (string-append #$output "/bin/" script-name)
+                                `("PATH" prefix (,guile-path ,(getenv "PATH")))
+                                `("GUILE_LOAD_PATH" prefix
+                                  (,(string-append #$output
+                                                   "/share/guile/site/"
+                                                   effective-version)
+                                   ,(getenv "GUILE_LOAD_PATH")))
+                                `("GUILE_LOAD_COMPILED_PATH" prefix
+                                  (,(string-append #$output "/lib/guile"
+                                                   effective-version
+                                                   "/site-ccache")
+                                   ,(getenv "GUILE_LOAD_COMPILED_PATH")))
+                                `("GUILE_AUTO_COMPILE" ":" = ("0"))))
+                            (list "lmdb-publishdata-export"
+                                  "gn-guile"))))))))
       (propagated-inputs
        ;; TODO: remove openssh-sans-x on next update to newer
        ;; guix-bioinformatics commit, i.e. newer than commit