gn: Initial ucsc-genome-browser and service.

2 files changed, 179 insertions, 0 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c899615..76406db 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -33,6 +33,7 @@
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages linux)
@@ -49,9 +50,12 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages rsync)
   #:use-module (gnu packages ruby)
+  #:use-module (gnu packages shells)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web))
 
@@ -1563,3 +1567,90 @@ multiple sequence alignment.")
         license:gpl3+   ; all sdsl-lite copies
         license:zlib    ; deps/sonLib/externalTools/cutest
         license:boost1.0)))) ; catch.hpp
+
+(define-public ucsc-genome-browser
+  (package
+    (name "ucsc-genome-browser")
+    (version "413")
+    (source (origin
+      (method git-fetch)
+      (uri (git-reference
+             (url "https://genome-source.gi.ucsc.edu/kent.git/")
+             (commit (string-append "v" version "_base"))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32 "1qcjhd4wcajik71z5347fw2sfhfkv0p6y7yldrrkmycw2qhqmpzn"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; fix later
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (add-before 'build 'pre-build
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               ;; Start by setting some variables.
+               (chdir "src")
+               (setenv "CC" ,(cc-for-target))
+               (setenv "HOME" (getcwd))
+
+               ;; And here we set the output directories
+               (setenv "CGI_BIN" (string-append out "/cgi-bin"))
+               (setenv "CGI_BIN_USER" (string-append out "/cgi-bin"))
+               (setenv "DOCUMENTROOT" (string-append out "/html"))
+               (setenv "DOCUMENTROOT_USER" (string-append out "/html"))
+               (setenv "BINDIR" (string-append out "/bin"))
+
+               ;; 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"))
+
+               #t)))
+         ;; Install happens during the 'build phase.
+         ;; Install the website files too
+         ;; rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/html/
+         (replace 'install
+           (lambda _
+             (invoke "make" "doc-install")
+             #t)))))
+    (inputs
+     `(("libpng" ,libpng)
+       ("mysql:dev" ,mariadb "dev")
+       ("mysql:lib" ,mariadb "lib")
+       ("openssl" ,openssl)
+       ("perl" ,perl)
+       ("python2" ,python-2)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(;("python" ,python)
+       ("rsync" ,rsync)    ; For installing js files from the source checkout
+       ;("tcl" ,tcl)
+       ;("tcsh" ,tcsh)
+       ("util-linux:lib" ,util-linux "lib")
+       ("which" ,(@ (gnu packages base) which))))
+    (home-page "https://www.genome.ucsc.edu/")
+    (synopsis "Structural variants detector for next-gen sequencing data")
+    (description
+     "The UCSC Genome Browser provides a rapid and reliable display of any
+requested portion of genomes at any scale, together with dozens of aligned
+annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands,
+assembly gaps and coverage, chromosomal bands, mouse homologies, and more).
+Half of the annotation tracks are computed at UCSC from publicly available
+sequence data.  The remaining tracks are provided by collaborators worldwide.
+Users can also add their own custom tracks to the browser for educational or
+research purposes.
+The Genome Browser stacks annotation tracks beneath genome coordinate positions,
+allowing rapid visual correlation of different types of information.  The user
+can look at a whole chromosome to get a feel for gene density, open a specific
+cytogenetic band to see a positionally mapped disease gene candidate, or zoom in
+to a particular gene to view its spliced ESTs and possible alternative splicing.
+The Genome Browser itself does not draw conclusions; rather, it collates all
+relevant information in one location, leaving the exploration and interpretation
+to the user.")
+    (license (license:non-copyleft
+               "https://www.genome.ucsc.edu/conditions.html"
+               "Free for academic/non-profit/personal use only."))))
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm
new file mode 100644
index 0000000..961569a
--- /dev/null
+++ b/gn/services/genome-browser.scm
@@ -0,0 +1,88 @@
+(define-module (gn services genome-browser))
+
+(use-modules (gnu)
+             (gn packages bioinformatics)
+             )
+(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")))
+
+;; TODO: create 'daily clean' mcron scripts.
+
+(define ucsc-genome-browser-port 4321)
+
+(operating-system
+  (host-name "genome-browser")
+  (timezone "Etc/UTC")
+  (locale "en_US.utf8")
+
+  (bootloader (bootloader-configuration
+               (bootloader grub-bootloader)
+               (target "does-not-matter")))
+  (file-systems %base-file-systems)
+  ;; No firmware for VMs
+  (firmware '())
+  (packages (cons* %base-packages))
+  (services
+    (list (service httpd-service-type
+                   (httpd-configuration
+                     (config
+                       (httpd-config-file
+                         (document-root (file-append ucsc-genome-browser "/html"))
+                         (listen (list (number->string ucsc-genome-browser-port)))
+                         (modules
+                           (cons*
+                             (httpd-module
+                               (name "cgid_module")
+                               (file "modules/mod_cgid.so"))
+                             (httpd-module
+                               (name "include_module")
+                               (file "modules/mod_include.so"))
+                             %default-httpd-modules))
+                         (extra-config (list "\
+TypesConfig etc/httpd/mime.types
+# 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 /htdocs " ucsc-genome-browser "/htdocs
+  <Directory " ucsc-genome-browser "/html>
+    Options +Includes
+    SSILegacyExprParser on
+  </Directory>
+
+  ScriptAlias /cgi-bin/ " ucsc-genome-browser "/cgi-bin/
+  <Directory " ucsc-genome-browser "/cgi-bin>
+    AllowOverride None
+    Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
+    SetHandler cgi-script
+    Require all granted
+  </Directory>
+
+  <Directory /var/www/html/trash>
+    Options MultiViews
+    AllowOverride None
+    Order allow,deny
+    Allow from all
+  </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
+;; xdg-open http://localhost:4321