From 477b95399080a23b32c350b9ed8629898d033a9b Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 25 Apr 2021 14:33:36 +0300
Subject: gn: ucsc genome browser: functioning web service?

---
 gn/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++-
 gn/services/genome-browser.scm | 43 ++++++++++++++++++++++++++----------------
 2 files changed, 53 insertions(+), 17 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 76406db..b836ff0 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1616,7 +1616,32 @@ multiple sequence alignment.")
          (replace 'install
            (lambda _
              (invoke "make" "doc-install")
-             #t)))))
+             #t))
+         ;; TODO: Figure out how to make this configurable in the service.
+         (add-after 'install 'create-hg-conf
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (with-output-to-file (string-append out "/cgi-bin/hg.conf")
+                 (lambda ()
+                   (display
+                     (string-append
+                     "browser.documentRoot=" out "/html\n"
+                     "db.host=gbdb\n"
+                     "db.user=admin\n"
+                     "db.password=admin\n"
+                     "db.trackDb=trackDb\n"
+                     "defaultGenome=Human\n"
+                     "central.db=hgcentral\n"
+                     "central.host=gbdb\n"
+                     "central.user=admin\n"
+                     "central.password=admin\n"
+                     "central.domain=\n"
+                     "backupcentral.db=hgcentral\n"
+                     "backupcentral.host=gbdb\n"
+                     "backupcentral.user=admin\n"
+                     "backupcentral.password=admin\n"
+                     "backupcentral.domain=\n"))))
+               #t))))))
     (inputs
      `(("libpng" ,libpng)
        ("mysql:dev" ,mariadb "dev")
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm
index 961569a..58c8e4a 100644
--- a/gn/services/genome-browser.scm
+++ b/gn/services/genome-browser.scm
@@ -1,3 +1,5 @@
+;; See dockerfile for some clarification about choices:
+;; https://github.com/icebert/docker_ucsc_genome_browser/blob/master/Dockerfile
 (define-module (gn services genome-browser))
 
 (use-modules (gnu)
@@ -6,24 +8,26 @@
 (use-service-modules web)
 
 (define %hg.conf
-  (plain-file "hg.conf"
-              (string-append "db.host=gbdb\n"
-                             "db.user=admin\n"
-                             "db.password=admin\n"
-                             "db.trackDb=trackDb\n"
-                             "defaultGenome=Human\n"
-                             "central.db=hgcentral\n"
-                             "central.host=gbdb\n"
-                             "central.user=admin\n"
-                             "central.password=admin\n"
-                             "central.domain=\n"
-                             "backupcentral.db=hgcentral\n"
-                             "backupcentral.host=gbdb\n"
-                             "backupcentral.user=admin\n"
-                             "backupcentral.password=admin\n"
-                             "backupcentral.domain=\n")))
+  (mixed-text-file "hg.conf"
+                   "browser.documentRoot=" ucsc-genome-browser "/html\n"
+                   "db.host=gbdb\n"
+                   "db.user=admin\n"
+                   "db.password=admin\n"
+                   "db.trackDb=trackDb\n"
+                   "defaultGenome=Human\n"
+                   "central.db=hgcentral\n"
+                   "central.host=gbdb\n"
+                   "central.user=admin\n"
+                   "central.password=admin\n"
+                   "central.domain=\n"
+                   "backupcentral.db=hgcentral\n"
+                   "backupcentral.host=gbdb\n"
+                   "backupcentral.user=admin\n"
+                   "backupcentral.password=admin\n"
+                   "backupcentral.domain=\n"))
 
 ;; TODO: create 'daily clean' mcron scripts.
+;;       /var/www/html/trash needs to be created and owned by httpd:httpd
 
 (define ucsc-genome-browser-port 4321)
 
@@ -57,11 +61,15 @@
                              %default-httpd-modules))
                          (extra-config (list "\
 TypesConfig etc/httpd/mime.types
+# cgid.sock needs to be creatable, not in the store
+ScriptSock /var/run/cgid.sock
 # same as 'listen' above
 <VirtualHost *:" (number->string ucsc-genome-browser-port) ">
   XBitHack On
   DocumentRoot " ucsc-genome-browser "/html
   Alias /bin " ucsc-genome-browser "/bin
+  Alias /cgi-bin " ucsc-genome-browser "/cgi-bin
+  #Alias /cgi-bin/hg.conf " %hg.conf "  # this doesn't seem to work
   Alias /htdocs " ucsc-genome-browser "/htdocs
   <Directory " ucsc-genome-browser "/html>
     Options +Includes
@@ -72,6 +80,8 @@ TypesConfig etc/httpd/mime.types
   <Directory " ucsc-genome-browser "/cgi-bin>
     AllowOverride None
     Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
+    #Order allow,deny
+    #Allow from all
     SetHandler cgi-script
     Require all granted
   </Directory>
@@ -85,4 +95,5 @@ TypesConfig etc/httpd/mime.types
 </VirtualHost>")))))))))
 
 ;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genome-browser.scm --network
+;; ALSO need to share in the external database
 ;; xdg-open http://localhost:4321
-- 
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