;; 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) #: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 node) #: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 "11d543eeca08fe0df4bf2be7222234fadb516a51") (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 "14b0lm964b3r8d444c1g6vbdmwdj58ff1hpxz61w4fblyg8jy7jz")))) (inputs (list python-click)) (native-inputs (list python-hypothesis python-mypy python-mypy-extensions python-pylint)) (propagated-inputs (list csvdiff diffutils gemma-wrapper gn-rust-correlation python-argon2-cffi python-authlib python-bcrypt ;; Replace use of bcrypt with argon python-biopython python-email-validator python-flask python-flask-cors python-lmdb python-mysqlclient python-numpy python-pandas python-pingouin-without-tests python-plotly python-pyld python-pymonad python-pytest python-pytest-mock python-redis python-requests python-scikit-learn python-scipy python-sparqlwrapper python-wrapper python-xapian-bindings r r-ctl r-optparse r-qtl r-rjson r-stringi r-wgcna rust-qtlreaper)) (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 "ae572dfe805defc4d40d173325178f5b08c080bf") (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 "0d93p4wpc5icikq395975y4bcw95j17x5m5f91r4gxrf8v79s0kb")))) (native-inputs (list graphviz)) (propagated-inputs (list genenetwork3 coreutils gemma gemma-wrapper git glibc-utf8-locales gn-rust-correlation grep gunicorn javascript-ace javascript-bootstrap javascript-chroma javascript-ckeditor javascript-colorbox javascript-cytoscape javascript-cytoscape-panzoom javascript-cytoscape-qtip javascript-d3-tip javascript-d3js ;; very old javascript-d3js-7 javascript-d3panels javascript-datatables javascript-datatables-buttons javascript-datatables-buttons-bootstrap javascript-datatables-buttons-styles javascript-datatables-col-reorder javascript-datatables-col-resize javascript-datatables-plugins javascript-datatables-scroller javascript-diff javascript-diff2html javascript-diff2html-ui javascript-font-awesome javascript-htmx javascript-highlight javascript-highlight-ui javascript-jquery javascript-jquery-cookie javascript-jquery-ui javascript-jscolor javascript-jszip javascript-linkify javascript-linkify-html javascript-marked javascript-marked-highlight javascript-nouislider javascript-nvd3 javascript-plotly javascript-purescript-genome-browser javascript-qtip2 javascript-shapiro-wilk javascript-twitter-post-fetcher javascript-typeahead javascript-uikit javascript-underscore-string javascript-zxcvbn js-jstat js-md5 js-parsley js-smart-time-ago js-underscore mariadb nginx parallel plink-ng-gn python-authlib python-autopep8 python-beautifulsoup4 python-configparser python-coverage python-cssselect python-flask python-flask-debugtoolbar python-flask-session python-htmlgen python-ijson python-jinja2 python-lxml python-markdown python-mypy python-mysqlclient python-numpy python-pandas python-pillow python-pylint python-pymonad python-pytest python-pytest-mock python-rdflib python-redis python-requests python-rpy2 python-scipy python-setuptools python-simplejson python-sqlalchemy python-wrapper python-xlsxwriter r r-ctl r-qtl r-wgcna redis rust-qtlreaper which ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit )) (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"))) (substitute* "gn2/wqflask/app_errors.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 genenetwork3-stable (let ((commit "e5569c3bb1c0d59ff7142273c5f51fe19f06cfe8") (revision "1")) (package (inherit genenetwork3) (name "genenetwork3-stable") (version (string-append (git-version "3.11" revision commit))) (arguments (list #:tests? #f #:phases #~(modify-phases %standard-phases (add-before 'build 'update-paths (lambda _ (for-each (lambda (fn) (substitute* (string-append "gn3/" fn) (("scripts/") (string-append #$output "/scripts/")))) '("api/rqtl.py" "computations/wgcna.py" "computations/ctl.py" "api/general.py")))) (add-before 'install 'install-scripts (lambda _ (begin (mkdir (string-append #$output "scripts")) (for-each (lambda (fn) (install-file fn (string-append #$output "/scripts"))) '("scripts/rqtl_wrapper.R" "scripts/ctl_analysis.R" "scripts/wgcna_analysis.R" )))))))) (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") (branch "prod")))))) (define-public genenetwork2-stable (let ((commit "95e634ca90d52922812b93df162686b348288651") (revision "1")) (package (inherit genenetwork2) (name "genenetwork2-stable") (version (string-append "stable-" (git-version "3.12" revision commit))) (source (git-checkout (url "https://github.com/genenetwork/genenetwork2") (branch "prod"))) (arguments (list #:tests? #f #:phases #~(modify-phases %standard-phases (add-before 'build 'update-font-paths (lambda* (#:key inputs outputs #:allow-other-keys) (for-each (lambda (fn) (substitute* (string-append "gn2/" fn) (("\\./gn2/wqflask/static/fonts/") (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts/")))) '("utility/Plot.py" "wqflask/marker_regression/display_mapping_results.py")))) )))))) (define-public gn-uploader (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") (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 "1q04viyf7d0q30k3424hrzsh9wxhhgs7hywlhzl3m68jki4zq1i7"))))) (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-authlib python-pymonad python-jsonpickle python-mysqlclient python-flask-session javascript-jquery javascript-bootstrap node-resumablejs)) (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 (let ((commit "12edc160df0ead9ac1ae4e62a44d49582e063021") (revision "01")) (package (name "gn-auth") (version (git-version "1.0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://git.genenetwork.org/gn-auth") (commit commit))) (hash (content-hash (base32 "11kixqv3rwfaad43bcqyh085gb0jfcpvzrlx66grkk73cqydgyzl"))))) (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-blinker 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)))