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authorEfraim Flashner2021-04-22 20:33:14 +0300
committerEfraim Flashner2021-04-22 20:35:59 +0300
commit765ea0a57cdc89c5dabccf4a4a398b80c8267449 (patch)
tree94aa52e410ffd027ceeb2a325d2c0d145b95844c /gn
parenta5c2123037175dcfea827444a325c839b8f7d05b (diff)
downloadguix-bioinformatics-765ea0a57cdc89c5dabccf4a4a398b80c8267449.tar.gz
gn: Initial ucsc-genome-browser and service.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm91
-rw-r--r--gn/services/genome-browser.scm88
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