gn: genome browser: nearly have the graph working.

2 files changed, 98 insertions, 51 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index b836ff0..3785b0f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -54,6 +54,7 @@
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tcl)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages vim)
@@ -1601,13 +1602,25 @@ multiple sequence alignment.")
                (setenv "DOCUMENTROOT_USER" (string-append out "/html"))
                (setenv "BINDIR" (string-append out "/bin"))
 
-               ;; Now let's fix some errors
+               ;; Now let's fix some errors:
                (mkdir-p (string-append out "/cgi-bin"))
                (substitute* "inc/cgi_build_rules.mk"
                   (("rm -f.*") ""))
                (substitute* (cons* "inc/cgi_build_rules.mk"
                                    (find-files "." "makefile"))
                   (("CGI_BIN\\}-\\$\\{USER") "CGI_BIN_USER"))
+               ;; Force linking with freetype.
+               (substitute* "inc/common.mk"
+                 (("libpng-config --ldflags") "pkg-config --libs libpng freetype2")
+                 (("libpng-config --I_opts") "pkg-config --cflags-only-I libpng freetype2"))
+               ;; Force the trash location.
+               (substitute* (cons*
+                              "utils/qa/showTracks"
+                              "webBlat/webBlat.cfg"
+                              "hg/js/hgTracks.js"
+                              (find-files "." "\\.c$"))
+                 ;; This line is specifically needed as-is.
+                 (("\\.\\./trash") "/var/www/html/trash"))
 
                #t)))
          ;; Install happens during the 'build phase.
@@ -1617,33 +1630,28 @@ multiple sequence alignment.")
            (lambda _
              (invoke "make" "doc-install")
              #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))))))
+                     "include /var/lib/genome/hg.conf\n")))
+               #t)))
+         (add-after 'install 'create-symlink
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               ;; Some trash locations are hardcoded as "../trash"
+               ;(symlink "/var/www/html/trash"
+               ;         (string-append out "/trash"))
+               (symlink "../html"
+                        (string-append out "/htdocs"))
+               #t)))
+         )))
     (inputs
-     `(("libpng" ,libpng)
+     `(
+       ("freetype" ,freetype)
+       ("libpng" ,libpng)
        ("mysql:dev" ,mariadb "dev")
        ("mysql:lib" ,mariadb "lib")
        ("openssl" ,openssl)
@@ -1651,10 +1659,11 @@ multiple sequence alignment.")
        ("python2" ,python-2)
        ("zlib" ,zlib)))
     (native-inputs
-     `(;("python" ,python)
+     `(("pkg-config" ,pkg-config)
+       ("python" ,python)
        ("rsync" ,rsync)    ; For installing js files from the source checkout
-       ;("tcl" ,tcl)
-       ;("tcsh" ,tcsh)
+       ("tcl" ,tcl)
+       ("tcsh" ,tcsh)
        ("util-linux:lib" ,util-linux "lib")
        ("which" ,(@ (gnu packages base) which))))
     (home-page "https://www.genome.ucsc.edu/")
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm
index 58c8e4a..7f7ffc0 100644
--- a/gn/services/genome-browser.scm
+++ b/gn/services/genome-browser.scm
@@ -1,30 +1,59 @@
 ;; See dockerfile for some clarification about choices:
 ;; https://github.com/icebert/docker_ucsc_genome_browser/blob/master/Dockerfile
+;; http://genome.ucsc.edu/goldenPath/help/mirrorManual.html
 (define-module (gn services genome-browser))
 
 (use-modules (gnu)
-             (gn packages bioinformatics)
-             )
-(use-service-modules web)
+             (guix packages)
+             (gn packages bioinformatics))
+(use-service-modules
+  databases
+  web)
+(use-package-modules
+  bash
+  databases
+  ghostscript
+  wget)
 
 (define %hg.conf
   (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.host=localhost\n"
+                   "db.user=readonly\n"
+                   "db.password=access\n"
                    "db.trackDb=trackDb\n"
-                   "defaultGenome=Human\n"
+                   "gbdbLoc1=/gbdb/\n"
+                   "gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/\n"
+                   ;# To disable on-the-fly loading of mysql data, comment out these lines.
+                   "slow-db.host=genome-mysql.soe.ucsc.edu\n"
+                   "slow-db.user=genomep\n"
+                   "slow-db.password=password\n"
+                   "defaultGenome=Mouse\n"
                    "central.db=hgcentral\n"
-                   "central.host=gbdb\n"
-                   "central.user=admin\n"
-                   "central.password=admin\n"
+                   "central.host=localhost\n"
+                   "central.socket=/run/mysqld/mysqld.sock\n"   ; default for mysql service
+                   "central.user=readwrite\n"
+                   "central.password=update\n"
                    "central.domain=\n"
                    "backupcentral.db=hgcentral\n"
-                   "backupcentral.host=gbdb\n"
-                   "backupcentral.user=admin\n"
-                   "backupcentral.password=admin\n"
-                   "backupcentral.domain=\n"))
+                   "backupcentral.host=localhost\n"
+                   "backupcentral.user=readwrite\n"
+                   "backupcentral.password=update\n"
+                   "backupcentral.domain=\n"
+                   "freeType=on\n"
+                   "freeTypeDir=" gs-fonts "/share/fonts/type1/ghostscript\n"
+                   "hgc.ghostscriptPath=" ghostscript "/bin/gs\n"   ; needed?
+                   ))
+
+(define %startup-script
+  (mixed-text-file "create_databases.sh"
+                   wget "/bin/wget http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql\n"
+                   bash-minimal "/bin/sh " (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh\n"
+                   mariadb "/bin/mysql -e \"create database hgcentral;\" mysql\n"
+                   mariadb "/bin/mysql hgcentral < hgcentral.sql\n"
+                   coreutils-minimal "/bin/mkdir -p /var/www/html/trash\n"
+                   coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n"
+                   ))
 
 ;; TODO: create 'daily clean' mcron scripts.
 ;;       /var/www/html/trash needs to be created and owned by httpd:httpd
@@ -42,13 +71,19 @@
   (file-systems %base-file-systems)
   ;; No firmware for VMs
   (firmware '())
-  (packages (cons* %base-packages))
+  (packages (cons* mariadb  ; for create-db script
+                   %base-packages))
   (services
-    (list (service httpd-service-type
+    (list (service mysql-service-type)
+          (service special-files-service-type
+                   `(("/root/create_hgcentral" ,%startup-script)
+                     ("/var/lib/genome/hg.conf" ,%hg.conf)))
+          (service httpd-service-type
                    (httpd-configuration
                      (config
                        (httpd-config-file
                          (document-root (file-append ucsc-genome-browser "/html"))
+                         (server-name "Genome_Browser")
                          (listen (list (number->string ucsc-genome-browser-port)))
                          (modules
                            (cons*
@@ -68,22 +103,25 @@ ScriptSock /var/run/cgid.sock
   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 /cgi-bin " ucsc-genome-browser "/cgi-bin   # causes cgi scripts to fail to render
   Alias /htdocs " ucsc-genome-browser "/htdocs
   <Directory " ucsc-genome-browser "/html>
-    Options +Includes
-    SSILegacyExprParser on
+    Options +Includes +FollowSymLinks +Indexes
+    AllowOverride None
+    <IfModule mod_authz_host.c>
+      Require all granted
+      SSILegacyExprParser on
+    </IfModule>
   </Directory>
 
-  ScriptAlias /cgi-bin/ " ucsc-genome-browser "/cgi-bin/
+  ScriptAlias /cgi-bin " ucsc-genome-browser "/cgi-bin
   <Directory " ucsc-genome-browser "/cgi-bin>
     AllowOverride None
-    Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
-    #Order allow,deny
-    #Allow from all
-    SetHandler cgi-script
+    Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks
+    Order allow,deny
+    #SetHandler cgi-script
     Require all granted
+    Allow from all
   </Directory>
 
   <Directory /var/www/html/trash>
@@ -94,6 +132,6 @@ ScriptSock /var/run/cgid.sock
   </Directory>
 </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
+;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genome-browser.scm --network ;--expose=/path/to/gbdb=/gbdb
+;; ALSO need to share in the external database?
 ;; xdg-open http://localhost:4321