;; Bioinformatics module (define-module (gn packages genenetwork) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (guix graph) #:use-module (guix scripts graph) #:use-module (guix store) #:use-module (guix gexp) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages check) #:use-module (gnu packages cran) #:use-module (gnu packages crates-io) #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages ghostscript) #:use-module (gnu packages golang) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) #:use-module (gnu packages parallel) #:use-module (gnu packages python) #:use-module (gnu packages python-check) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages rdf) #:use-module (gnu packages rust) #:use-module (gnu packages scheme) #:use-module (gnu packages statistics) #:use-module (gnu packages version-control) ; #:use-module (gnu packages vim) #:use-module (gnu packages web) ; #:use-module (gnu packages wget) #:use-module (gnu packages xml) #:use-module (gn packages bioinformatics) #:use-module (gn packages gemma) #:use-module (gn packages javascript) #:use-module (gn packages python) #:use-module (gn packages statistics) #:use-module (gn packages twint) #:use-module (gn packages web) #:use-module (srfi srfi-1)) (define-public rust-qtlreaper (let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3") (revision "1")) (package (name "rust-qtlreaper") (version "0.1.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/chfi/rust-qtlreaper.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0h70aalsplmc6xn1w7ha102n3bsi3gqkbnbrjvjm2za37c07gv0g")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-rand" ,rust-rand-0.6) ("rust-structopt" ,rust-structopt-0.2) ("rust-rayon" ,rust-rayon-1) ("rust-serde" ,rust-serde-1) ("rust-serde-json" ,rust-serde-json-1) ("rust-ndarray" ,rust-ndarray-0.12)) #:phases (modify-phases %standard-phases ;; Test results vary based on the machine running them. (replace 'check (lambda _ (or (assoc-ref %standard-phases 'check) (begin (substitute* "src/geneobject.rs" ;; array![Genotype::Unk, Genotype::Unk, Genotype::Pat] (("0.3421367343627405") "0.3421367343627406") ;; array![Genotype::Unk, Genotype::Unk, Genotype::Unk] (("-0.3223330030526561") "-0.32233300305265566")) (assoc-ref %standard-phases 'check))) #t))))) (home-page "https://github.com/chfi/rust-qtlreaper") (synopsis "Reimplementation of genenetwork/QTLReaper in Rust") (description "Reimplementation of genenetwork/QTLReaper in Rust") (license #f)))) (define-public genenetwork3 (let ((commit "77c274b79c3ec01de60e90db3299763cb58f715b")) (package (name "genenetwork3") (version (string-append "0.0.1-guix-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/genenetwork3.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0ha70ibr7dqz0kzmgccx5l6nrmmf2a2mj7scg6jllx232crjby72")))) (propagated-inputs `(("coreutils" ,coreutils) ("gemma-wrapper" ,gemma-wrapper) ("csvdiff" ,go-github-com-aswinkarthik-csvdiff) ("python" ,python-wrapper) ("python-bcrypt" ,python-bcrypt) ("python-flask" ,python-flask) ("python-flask-cors" ,python-flask-cors) ("python-ipfshttpclient" ,python-ipfshttpclient) ("python-mypy" ,python-mypy) ("python-mypy-extensions" ,python-mypy-extensions) ("python-mysqlclient" ,python-mysqlclient) ("python-numpy" ,python-numpy) ("python-pylint" ,python-pylint) ("python-redis" ,python-redis) ("python-requests" ,python-requests) ("python-scipy" ,python-scipy) ("python-plotly" ,python-plotly) ("python-sqlalchemy-stubs" ,python-sqlalchemy-stubs) ("r-optparse" ,r-optparse) ("r-qtl" ,r-qtl) ("r-stringi" ,r-stringi) ("r-wgcna" ,r-wgcna) ("r-rjson" ,r-rjson))) (build-system python-build-system) (home-page "https://github.com/genenetwork/genenetwork3") (synopsis "GeneNetwork3 API for data science and machine learning.") (description "GeneNetwork3 API for data science and machine learning.") (license license:agpl3+)))) (define-public genenetwork2 (let ((commit "fe345c9f2e99be748511f6889420d6560a553a37")) (package (name "genenetwork2") (version (string-append "3.11-guix-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/genenetwork2.git") (commit commit))) (file-name (string-append name "-" version)) (sha256 (base32 "1y6psmxpm3qn78dx6xfc11rdpf22vf807qb7grnp82gl19q6408w")))) (native-inputs `(("graphviz" ,graphviz) ;; And the graphs ;("genenetwork-graph" ,genenetwork-graph) ;("dag-svg-file" ,dag-svg-file) )) (propagated-inputs `(("genenetwork3" ,genenetwork3) ("parallel" ,parallel) ;; GNU parallel ("coreutils" ,coreutils) ("git" ,git) ("which" ,which) ("grep" ,grep) ("r" ,r) ("r-ctl" ,r-ctl) ; ("r-phewas" ,r-phewas) ("r-qtl" ,r-qtl) ("r-wgcna" ,r-wgcna) ("redis" ,redis) ("mariadb" ,mariadb) ("gemma" ,gemma-gn2) ("gemma-wrapper" ,gemma-wrapper) ; ("genenetwork2-files-small" ,genenetwork2-files-small) ("plink-ng-gn" ,plink-ng-gn) ; ("pylmm-gn2" ,pylmm-gn2) ("rust-qtlreaper" ,rust-qtlreaper) ("glibc-utf8-locales" ,glibc-utf8-locales) ("nginx" ,nginx) ("python" ,python-wrapper) ("python-pillow" ,python-pillow) ("python-coverage" ,python-coverage) ("python-configparser" ,python-configparser) ;; maintenance/scripts ("python-flask" ,python-flask) ("gunicorn" ,gunicorn) ("python-autopep8" ,python-autopep8) ("python-cssselect" ,python-cssselect) ("python-flask-debugtoolbar" ,python-flask-debugtoolbar) ("python-elasticsearch" ,python-elasticsearch) ("python-htmlgen" ,python-htmlgen) ("python-jinja2" ,python-jinja2) ("python-sqlalchemy" ,python-sqlalchemy) ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) ("python-setuptools" ,python-setuptools) ("python-scipy" ,python-scipy) ("python-lxml" ,python-lxml) ("python-mechanize" ,python-mechanize) ("python-mysqlclient" ,python-mysqlclient) ("python-mypy" ,python-mypy) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-parameterized" ,python-parameterized) ("python-passlib" ,python-passlib) ("python-pylint" ,python-pylint) ("python-redis" ,python-redis) ("python-requests" ,python-requests) ("python-simplejson" ,python-simplejson) ("python-pyyaml" ,python-pyyaml) ("python-markdown" ,python-markdown) ("python-rdflib" ,python-rdflib) ("python-twint" ,python-twint) ("python-unittest2" ,python-unittest2) ;; TODO: Get rid of Python R bindings ("python-rpy2" ,python-rpy2-next) ("python-beautifulsoup4" ,python-beautifulsoup4) ;; Disable for now. Build fails on Penguin2 ;; ("python-flask-socketio" ,python-flask-socketio) ("python-xlsxwriter" ,python-xlsxwriter) ;; All the external js dependencies ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) ("javascript-cytoscape" ,javascript-cytoscape) ("javascript-panzoom" ,javascript-cytoscape-panzoom) ("javascript-qtip" ,javascript-cytoscape-qtip) ("javascript-chroma" ,javascript-chroma) ("javascript-d3-tip" ,javascript-d3-tip) ("javascript-jscolor" ,javascript-jscolor) ("javascript-colorbox" ,javascript-colorbox) ("javascript-jszip" ,javascript-jszip) ("js-jstat" ,js-jstat) ("js-md5" ,js-md5) ("js-parsley" ,js-parsley) ("javascript-plotly" ,javascript-plotly) ("javascript-typeahead" ,javascript-typeahead) ("js-underscore" ,js-underscore) ("js-smart-time-ago" ,js-smart-time-ago) ("javascript-nouislider" ,javascript-nouislider) ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) ("javascript-ckeditor" ,javascript-ckeditor) ("javascript-datatables" ,javascript-datatables) ("javascript-datatables-scroller" ,javascript-datatables-scroller) ("javascript-datatables-buttons" ,javascript-datatables-buttons) ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) ("javascript-datatables-plugins" ,javascript-datatables-plugins) ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) ("javascript-datatables-col-resize" ,javascript-datatables-col-resize) ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) ("javascript-underscore-string" ,javascript-underscore-string) ("javascript-qtip2" ,javascript-qtip2) ("javascript-d3js" ,javascript-d3js) ("javascript-nvd3" ,javascript-nvd3) ("javascript-bootstrap" ,javascript-bootstrap) ("javascript-jquery" ,javascript-jquery) ("javascript-zxcvbn" ,javascript-zxcvbn) ("javascript-jquery-ui" ,javascript-jquery-ui) ("javascript-jquery-cookie" ,javascript-jquery-cookie) ("javascript-font-awesome" ,javascript-font-awesome))) (inputs `(("javascript-colorbox" ,(package-source javascript-colorbox)))) (build-system python-build-system) (arguments `(#:tests? #f ; no 'setup.py test' #:phases (modify-phases %standard-phases (delete 'reset-gzip-timestamps) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" (("/usr/bin/env") (which "env")) (("python ") (string-append (which "python3") " ")) (("readlink") (which "readlink")) (("dirname") (which "dirname")) (("basename") (which "basename")) (("cat") (which "cat")) (("echo") (which "echo")) (("redis-server") (which "redis-server")) (("git") (which "git")) (("grep") (which "grep")) (("rm") (which "rm")) (("which") (which "which"))) #t)) ; (add-after 'unpack 'patch-javascript ; (lambda* (#:key inputs #:allow-other-keys) ; (let ((colorbox (assoc-ref inputs "javascript-colorbox")) ; (gn2 "/share/genenetwork2/javascript/")) ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") ; #t))) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ( ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) ) (substitute* '("etc/default_settings.py") ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) ) ))) ; (add-after 'install 'generate-graph ; (lambda* (#:key inputs outputs #:allow-other-keys) ; (call-with-output-file ; (string-append ; (assoc-ref outputs "out") ; "/lib/python" ; (python-version (assoc-ref inputs "python")) ; "/site-packages" ; "/wqflask/dependency-graph.html") ; (lambda (port) ; (format ; port "~a" ; ,(call-with-output-string ; (lambda (p) ; (with-output-to-port p ; (lambda () ; (run-with-store ; (open-connection) ; (export-graph ; (list this-package) ; p ; #:node-type %package-node-type ; #:backend %d3js-backend))))))))))) ;(add-after 'install 'generate-dag-svg-file ; (lambda* (#:key inputs outputs #:allow-other-keys) ; (let* ((output-dir ; (string-append ; (assoc-ref outputs "out") ; "/lib/python" ; (python-version (assoc-ref inputs "python")) ; "/site-packages/wqflask/")) ; (dot-file ; (string-append ; output-dir ; "dependency-graph.dot")) ; (svg-file ; (string-append ; output-dir ; "dependency-graph.svg"))) ; (begin ; (call-with-output-file ; dot-file ; (lambda (port) ; (format ; port "~a" ; ,(call-with-output-string ; (lambda (p) ; (with-output-to-port p ; (lambda () ; (run-with-store ; (open-connection) ; (export-graph ; (list this-package) ; p ; #:node-type %package-node-type ; #:backend %graphviz-backend))))))))) ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) ;; TODO: Use this to replace the two previous phases. ;(add-after 'install 'install-generated-files ; (lambda* (#:key inputs outputs #:allow-other-keys) ; (let ((output-dir ; (string-append ; (assoc-ref outputs "out") ; "/lib/python" ; (python-version (assoc-ref inputs "python")) ; "/site-packages/wqflask/"))) ; (install-file (string-append %dag-svg-file "/dependency-graph.dot") output-dir) ; (install-file (string-append %dag-svg-file "/dependency-graph.svg") output-dir) ; (install-file (string-append %genenetwork-graph "/dependency-graph.html") output-dir) ; #t))) (add-after 'install 'generate-dependency-file (lambda* (#:key inputs outputs #:allow-other-keys) (call-with-output-file (string-append (assoc-ref outputs "out") "/lib/python" (python-version (assoc-ref inputs "python")) "/site-packages" "/wqflask/DEPENDENCIES.md") (lambda (port) (format port " #### System Inputs (generated from ~a package defined in ~a) |Name | Description | |-----|-------------| ~a " ,(package-name this-package) (string-append "[genenetwork.scm]" "(http://git.genenetwork.org/" "guix-bioinformatics/guix-bioinformatics" "/src/branch/master/gn/packages/" "genenetwork.scm)") ,(apply string-append (map (lambda (input) (let* ((pkg (cadr input)) (name (package-name pkg)) (version (package-version pkg)) (home-page (package-home-page pkg)) (description (package-synopsis pkg))) (string-append "| **[" name "](" home-page ")** v" version"| " description " |\n"))) (package-propagated-inputs this-package))))))))))) (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") (license license:agpl3+)))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x (define-public genenetwork2-files-small (let ((pfff "xx")) (package (name "genenetwork2-files-small") (version "1.0") (source (origin (method url-fetch) (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") (file-name (string-append name "-" pfff)) (sha256 (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) (build-system trivial-build-system) (native-inputs `(("lz4" ,lz4) ("tar" ,tar) ("source" ,source))) (arguments `(#:modules ((guix build utils)) #:builder (let* ((out (assoc-ref %outputs "out")) (name "gn2_data_s") (tarfn (string-append name ".tar")) (targetdir (string-append out "/share/genenetwork2/"))) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))) (and (zero? (system* lz4unpack source "-d" tarfn)) (zero? (system* tar "xf" tarfn)) (mkdir-p targetdir) (copy-recursively name targetdir))))))) (home-page "http://genenetwork.org/") (synopsis "Small file archive to run on genenetwork") (description "Genenetwork genotype and mapping files.") (license license:agpl3+)))) (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) (package (name "genenetwork2-database-small") (version "1.0") (source (origin (method url-fetch) (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") (file-name (string-append name "-" md5)) (sha256 (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) (build-system trivial-build-system) (native-inputs `(("unzip" ,unzip) ("source" ,source))) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))) (and (mkdir "db") (zero? (system* unzip source "-d" "db")) (chdir "db")))))) (home-page "http://genenetwork.org/") (synopsis "Small database to run on genenetwork") (description "Genenetwork installation + database.") (license license:agpl3+)))) (define (genenetwork-graph) (with-imported-modules '((guix build utils)) (gexp->derivation "genenetwork-graph" #~(begin (use-modules (guix build utils) (srfi srfi-1)) (define (python-version package) (let* ((version (last (string-split package #\-))) (components (string-split version #\.)) (major+minor (take components 2))) (string-join major+minor "."))) (let ((html-file (string-append #$output "/lib/python" (python-version #$python) "/site-packages/wqflask" "/dependency-graph.html"))) (mkdir-p (dirname html-file)) (call-with-output-file html-file (lambda (port) (format port "~a" #$(call-with-output-string (lambda (p) (with-output-to-port p (lambda () (run-with-store (open-connection) (export-graph (list genenetwork2) p #:node-type %package-node-type #:backend %d3js-backend)))))))))))))) ;(define (computed-genenetwork-graph) ; (with-imported-modules '((guix build utils)) ; (computed-file "genenetwork-graph" ; #~(begin ; (use-modules (guix build utils)) ; (call-with-output-file #$output ; (lambda (port) ; (format ; port "~a" ; #$(call-with-output-string ; (lambda (p) ; (with-output-to-port p ; (lambda () ; (run-with-store ; (open-connection) ; (export-graph ; (list genenetwork1) ; p ; #:node-type %package-node-type ; #:backend %d3js-backend))))))))))))) (define (dag-svg-file) (with-imported-modules '((guix build utils)) (gexp->derivation "dag-svg-file" #~(begin (use-modules (guix build utils) (srfi srfi-1)) (define (python-version package) (let* ((version (last (string-split package #\-))) (components (string-split version #\.)) (major+minor (take components 2))) (string-join major+minor "."))) (let* ((dest-dir (string-append #$output "/lib/python" (python-version #$python) "/site-packages/wqflask")) (dot-file (string-append dest-dir "/dependency-graph.dot")) (svg-file (string-append dest-dir "/dependency-graph.svg"))) (mkdir-p dest-dir) (call-with-output-file dot-file (lambda (port) (format port "~a" #$(call-with-output-string (lambda (p) (with-output-to-port p (lambda () (run-with-store (open-connection) (export-graph (list genenetwork2) p #:node-type %package-node-type #:backend %graphviz-backend))))))))) (invoke #+(file-append graphviz "/bin/dot") "-Tsvg" "-o" svg-file dot-file)))))) ;(define-public genenetwork2-combined ; (directory-union ; "genenetwork2" ; (list genenetwork2 genenetwork-graph dag-svg-file)))