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| -rw-r--r-- | guix.scm | 187 |
1 files changed, 187 insertions, 0 deletions
diff --git a/guix.scm b/guix.scm new file mode 100644 index 0000000..6915ba3 --- /dev/null +++ b/guix.scm @@ -0,0 +1,187 @@ +;; +;; GeneCup guix.scm - package definition +;; +;; Build with: +;; +;; guix build -L ../guix-bioinformatics -L ../guix-past/modules \ +;; -L ../guix-rust-past-crates/modules -f guix.scm +;; +;; Development shell: +;; +;; guix shell -L ../guix-bioinformatics -L ../guix-past/modules \ +;; -L ../guix-rust-past-crates/modules -D -f guix.scm +;; + +(define-module (guix) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix build-system pyproject) + #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (gnu packages admin) + #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages compression) + #:use-module (gnu packages javascript) + #:use-module (gnu packages python) + #: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 python-check) + #:use-module (gnu packages python-build) + #:use-module (gnu packages time) + #:use-module (gn packages javascript) + #:use-module (gn packages web)) + +(define %source-dir (dirname (current-filename))) + +(define-public python-google-genai + (package + (name "python-google-genai") + (version "1.68.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "google_genai" version)) + (sha256 + (base32 "15na2kxak5farpm5az0dw7r3c3mf3nhy95rsk5r963v3pjwc0c5c")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f)) ; tests require network access and API keys + (propagated-inputs + (list python-google-auth + python-httpx + python-pydantic + python-requests + python-tenacity + python-websockets + python-typing-extensions + python-distro + python-sniffio)) + (native-inputs + (list python-setuptools + python-wheel)) + (home-page "https://github.com/googleapis/python-genai") + (synopsis "Google Generative AI Python SDK") + (description "Client library for the Google Generative AI API, providing +access to Gemini models.") + (license license:asl2.0))) + +(define-public genecup + (package + (name "genecup") + (version "0.0.1") + (source (local-file %source-dir #:recursive? #t)) + (build-system python-build-system) + (arguments + (list + #:tests? #f ; no test suite + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (add-after 'unpack 'make-files-writable + (lambda _ + (for-each make-file-writable (find-files ".")))) + (add-after 'unpack 'patch-sources + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((inetutils (assoc-ref inputs "inetutils"))) + (substitute* '("templates/cytoscape.html" + "templates/tableview.html" + "templates/tableview0.html" + "templates/userarchive.html") + (("https.*FileSaver.js.*\\\">") "/static/FileSaver.js\">") + (("https.*cytoscape-svg.js.*\\\">") "/static/cytoscape-svg.js\">") + (("https.*cytoscape.min.js.*\\\">") "/static/cytoscape.min.js\">")) + (substitute* "templates/layout.html" + (("https.*bootstrap.min.css.*\\\">") "/static/bootstrap.min.css\">") + (("https.*4.*bootstrap.min.js.*\\\">") "/static/bootstrap.min.js\">") + (("https.*4.7.0/css/font-awesome.min.css") "/static/font-awesome.min.css") + (("https.*jquery-3.2.1.slim.min.js.*\\\">") "/static/jquery.slim.min.js\">") + (("https.*1.12.9/umd/popper.min.js.*\\\">") "/static/popper.min.js\">"))))) + (add-after 'unpack 'extract-pubmed-archive + (lambda _ + (invoke "gzip" "-d" "minipubmed.tgz") + (invoke "tar" "xvf" "minipubmed.tar"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (copy-recursively "." out)))) + (add-after 'install 'install-javascript + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (awesome (assoc-ref inputs "font-awesome")) + (bootstrap (assoc-ref inputs "bootstrap")) + (cytoscape (assoc-ref inputs "cytoscape")) + (cytoscape-svg (assoc-ref inputs "cytoscape-svg")) + (jquery (assoc-ref inputs "jquery")) + (js-filesaver (assoc-ref inputs "js-filesaver")) + (js-popper (assoc-ref inputs "js-popper"))) + (symlink (string-append awesome + "/share/web/font-awesomecss/font-awesome.min.css") + (string-append out "/static/font-awesome.min.css")) + (symlink (string-append bootstrap + "/share/web/bootstrap/css/bootstrap.min.css") + (string-append out "/static/bootstrap.min.css")) + (symlink (string-append bootstrap + "/share/web/bootstrap/js/bootstrap.min.js") + (string-append out "/static/bootstrap.min.js")) + (symlink (string-append cytoscape + "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js") + (string-append out "/static/cytoscape.min.js")) + (symlink (string-append cytoscape-svg + "/share/javascript/cytoscape-svg.js") + (string-append out "/static/cytoscape-svg.js")) + (symlink (string-append jquery + "/share/web/jquery/jquery.slim.min.js") + (string-append out "/static/jquery.slim.min.js")) + (symlink (string-append js-filesaver + "/share/javascript/FileSaver.js") + (string-append out "/static/FileSaver.js")) + (symlink (string-append js-popper + "/share/javascript/popper.min.js") + (string-append out "/static/popper.min.js"))))) + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (path (getenv "GUIX_PYTHONPATH"))) + (wrap-program (string-append out "/server.py") + `("PATH" ":" prefix (,(dirname (which "edirect.pl")) + ,(dirname (which "dirname")) + ,(dirname (which "grep")) + ,(dirname (which "sed")))) + `("GUIX_PYTHONPATH" ":" prefix (,path))))))))) + (inputs + `(("edirect" ,edirect) + ("inetutils" ,inetutils) + ("gzip" ,gzip) + ("tar" ,tar) + ("python-bcrypt" ,python-bcrypt) + ("python-dotenv" ,python-dotenv) + ("python-flask" ,python-flask) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) + ("python-google-genai" ,python-google-genai) + ("python-nltk" ,python-nltk) + ("python-pandas" ,python-pandas) + ("python-pytz" ,python-pytz) + ;; JavaScript assets symlinked into static/ + ("bootstrap" ,web-bootstrap) + ("cytoscape" ,javascript-cytoscape-3.17) + ("cytoscape-svg" ,js-cytoscape-svg-vendor-0.3.1) + ("font-awesome" ,web-font-awesome) + ("jquery" ,web-jquery) + ("js-filesaver" ,js-filesaver-1.3.2) + ("js-popper" ,js-popper-1.12.9))) + (home-page "http://genecup.org") + (synopsis "GeneCup: gene-addiction relationship search using PubMed") + (description "GeneCup automatically extracts information from PubMed and +the NHGRI-EBI GWAS catalog on the relationship of any gene with a custom list +of keywords hierarchically organized into an ontology.") + (license license:expat))) + +genecup |