diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 91 | ||||
| -rw-r--r-- | gn/services/genome-browser.scm | 88 |
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 |