;; 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 (guix packages) #: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 machine-learning) #:use-module (gnu packages parallel) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #: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 search) #:use-module (gnu packages statistics) #:use-module (gnu packages textutils) #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gn packages bioinformatics) #:use-module (gn packages crates-io) #:use-module (gn packages gemma) #:use-module (gn packages javascript) #:use-module (gn packages python) #:use-module (gn packages statistics) #:use-module (gn packages web) #:use-module (gn packages python-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)))) ; Tests on the upstream python-pengouin package are broken. So, we ; create this temporary workaround. (define python-pingouin-without-tests (package (inherit python-pingouin) (arguments (substitute-keyword-arguments (package-arguments python-pingouin) ((#:tests? _ #f) #f))))) (define-public genenetwork3 (let ((commit "6bb4a5f05c1a2c96b7da1780ae4a1d70c7cc4afb") (revision "5")) (package (name "genenetwork3") (version (git-version "0.1.0" revision commit)) (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 "13nvi2gwwb0shra0d9rsfhppa9ky4bhgh1zgb34790ax0g9lwa97")))) (inputs (list python-click)) (native-inputs `(("python-hypothesis" ,python-hypothesis) ("python-mypy" ,python-mypy) ("python-mypy-extensions" ,python-mypy-extensions) ("python-pylint" ,python-pylint) ("python-pytest" ,python-pytest) ("python-pytest-mock" ,python-pytest-mock))) (propagated-inputs `(("gemma-wrapper" ,gemma-wrapper) ("python-wrapper" ,python-wrapper) ("csvdiff" ,csvdiff) ("gn-rust-correlation" ,gn-rust-correlation) ;; Replace use of bcrypt with argon below ("python-bcrypt" ,python-bcrypt) ("python-argon2-cffi" ,python-argon2-cffi) ("python-flask" ,python-flask) ("python-flask-cors" ,python-flask-cors) ;; Not working in Python > 3.8 ;; python-ipfshttpclient ("python-lmdb" ,python-lmdb) ("python-mysqlclient" ,python-mysqlclient) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ;; python-pingouin << build failing ("python-pingouin-without-tests" ,python-pingouin-without-tests) ("python-plotly" ,python-plotly) ("python-pyld" ,python-pyld) ("python-scikit-learn" ,python-scikit-learn) ("python-pymonad" ,python-pymonad) ("python-redis" ,python-redis) ("python-requests" ,python-requests) ("python-scipy" ,python-scipy) ("python-authlib" ,python-authlib) ("python-sparqlwrapper" ,python-sparqlwrapper) ("python-email-validator" ,python-email-validator) ("python-xapian-bindings" ,python-xapian-bindings) ("r-optparse" ,r-optparse) ("r-qtl" ,r-qtl) ("r-rjson" ,r-rjson) ("r-stringi" ,r-stringi) ("r-wgcna" ,r-wgcna) ("r-ctl" ,r-ctl) ("rust-qtlreaper" ,rust-qtlreaper) ("diffutils" ,diffutils))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-k" "unit_test"))))))) (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 "1e81c74ee8752ad2913b4e610ba7575638755385") (revision "4")) (package (name "genenetwork2") (version (git-version "3.11" revision commit)) (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 "18g4dd3h737slqmp1ql2jqqzmzql3mx3b4xy72d7qwhwwhc7hcgv")))) (native-inputs (list graphviz)) (propagated-inputs (list genenetwork3 parallel coreutils git which grep r r-ctl r-qtl r-wgcna redis mariadb gemma gemma-wrapper plink-ng-gn rust-qtlreaper gn-rust-correlation glibc-utf8-locales nginx python-wrapper python-pillow python-coverage python-configparser python-flask gunicorn python-autopep8 python-cssselect python-flask-debugtoolbar python-htmlgen python-ijson python-jinja2 python-pytest python-pytest-mock python-sqlalchemy python-setuptools python-scipy python-lxml python-mysqlclient python-mypy python-numpy python-pandas python-pylint python-pymonad python-redis python-requests python-simplejson python-markdown python-rdflib python-authlib python-flask-session python-rpy2 python-beautifulsoup4 python-xlsxwriter javascript-twitter-post-fetcher javascript-cytoscape javascript-cytoscape-panzoom javascript-cytoscape-qtip javascript-chroma javascript-d3-tip javascript-jscolor javascript-colorbox javascript-jszip js-jstat js-md5 js-parsley javascript-plotly javascript-typeahead js-underscore javascript-uikit js-smart-time-ago javascript-nouislider javascript-purescript-genome-browser javascript-ckeditor javascript-datatables javascript-datatables-scroller javascript-datatables-buttons javascript-datatables-buttons-bootstrap javascript-datatables-plugins javascript-datatables-col-reorder javascript-datatables-col-resize javascript-datatables-buttons-styles javascript-shapiro-wilk javascript-underscore-string javascript-htmx javascript-qtip2 javascript-d3js javascript-nvd3 javascript-bootstrap javascript-jquery javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit javascript-font-awesome)) (inputs (list javascript-colorbox)) (build-system python-build-system) (arguments (list #:tests? #f #:phases #~(modify-phases %standard-phases (delete 'reset-gzip-timestamps) (add-after 'unpack 'fix-paths-to-static-files (lambda* (#:key inputs outputs #:allow-other-keys) ;; Set absolute store paths to installed static files. (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" (("\\./gn2/wqflask/static/fonts") (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts"))) (substitute* "gn2/wqflask/views.py" (("\\./gn2/wqflask/static/gif/error") (string-append (site-packages inputs outputs) "/gn2/wqflask/static/gif/error"))))) (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"))))) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) (substitute* '("gn2/default_settings.py") (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))))))))) (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") (license license:agpl3+)))) (define-public gn-uploader (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") (version "0.0.1")) (package (name "gn-uploader") (version (string-append version "-" (string-take commit 8))) (source (origin (method git-fetch) (uri (git-reference (url "https://git.genenetwork.org/gn-uploader") (commit commit))) (hash (content-hash (base32 "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-m" "unit_test"))))))) (native-inputs (list python-mypy python-pylint python-pytest python-hypothesis)) (propagated-inputs (list gunicorn python-redis python-flask python-pyyaml python-jsonpickle python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, that does quality control for the data files that is being uploaded to ensure it fulfils all conditions before it can be accepted.") (home-page "https://git.genenetwork.org/gn-uploader") (license license:agpl3+)))) (define-public gn-auth (package (name "gn-auth") (version "1.0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) (hash (content-hash (base32 "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs (list python-hypothesis python-mypy python-mypy-extensions python-pylint python-pytest python-pytest-mock)) (propagated-inputs (list gunicorn python-argon2-cffi python-authlib python-email-validator python-flask python-flask-cors python-mysqlclient python-pymonad python-redis yoyo-migrations)) (home-page "https://github.com/genenetwork/gn-auth") (synopsis "Authentication and Authorisation server for GeneNetwork services") (description "Authentication and Authorisation server for GeneNetwork services.") (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)))