From 2955dd2850b81658c22f2d600805a204ef47b565 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 16 Mar 2021 06:48:49 -0500
Subject: gn: bnw: updates

wrap run_scripts for octave invocations with coreutils
adjust service
---
 gn/packages/bnw.scm           |  5 +++--
 gn/services/bnw-container.scm | 17 ++++++++++++-----
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index 842f327..f3f46d2 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -14,7 +14,7 @@
 
 (define-public bnw
   (let ((commit "f39cd7ba681262de5658cfe7b9b0d46c6000b4fa")
-        (revision "2"))
+        (revision "3"))
     (package
       (name "bnw")
       (version (git-version "genenet8_initial_1.3" revision commit)) ; Mar 4, 2021
@@ -229,6 +229,7 @@
                (for-each
                  (lambda (script)
                    (wrap-program script
+                    `("PATH" prefix (,(dirname (which "cp"))))
                     `("PYTHONPATH" prefix (,(getenv "PYTHONPATH")))))
                  (find-files (string-append (assoc-ref outputs "out")
                                             "/sourcecodes/run_scripts") "^run"))
@@ -248,7 +249,7 @@
                  (invoke "sh" "build.sh")))))))
       (inputs
        `(("graphviz" ,graphviz)
-         ("octave" ,octave)
+         ("octave" ,octave-cli)
          ("python" ,python)
          ("python-plotly" ,python-plotly)
          ("rmath" ,rmath-standalone)
diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm
index 4046a4f..b812652 100644
--- a/gn/services/bnw-container.scm
+++ b/gn/services/bnw-container.scm
@@ -2,6 +2,7 @@
 
 (use-modules (gnu)
              (gn packages bnw)
+             (guix build utils)
              (guix records)
              (ice-9 match))
 (use-service-modules networking web)
@@ -20,14 +21,18 @@
 
 (define bnw-activation
   (match-lambda
-    (($ <bnw-configuration> package deploy-directory port)
+    (($ <bnw-configuration> package _ port)
      #~(begin
-         (let ((genenet "/var/lib/genenet/bnw"))
-           ;(mkdir-p #$deploy-directory)
-           ;(copy-recursively #$package #$deploy-directory)
+         (let ((genenet "/var/lib/genenet/bnw")
+               (php-fpm-uid (passwd:uid (getpw "php-fpm")))
+               (php-fpm-gid (passwd:gid (getpw "php-fpm"))))
            (mkdir-p genenet)
            (copy-recursively #$(file-append package "/var_lib_genenet_bnw") genenet)
-           (invoke #$(file-append coreutils "/bin/chmod") "a+w" genenet))))))
+           (for-each (lambda (file-name)
+                       (make-file-writable file-name)
+                       (chown file-name php-fpm-uid php-fpm-gid))
+                     (find-files genenet
+                                 #:directories? #t)))))))
 
 (define bnw-nginx-config
   (match-lambda
@@ -85,3 +90,5 @@
                            ;(bnw-configuration
                            ;  (port '("8888")))
                            ))))
+
+;; guix system container -L ~/workspace/guix-past/modules/ -L ~/workspace/guix-bioinformatics/ ~/workspace/guix-bioinformatics/gn/services/bnw-container.scm --network
-- 
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