;;
;; GeneCup guix.scm - package definition
;;
;; Build with:
;;
;; guix build -f guix.scm
;;
;; Development shell:
;;
;; guix shell -L . -C -N -F --expose=$HOME/.config/gemini --share=/export3/PubMed edirect-25 genecup-gemini coreutils -- genecup --port 4201
;;
;; In a shell you can run
;;
;; guix shell -C -N -F -L . --expose=$HOME/.config/gemini --share=/export3/PubMed edirect-25 genecup-gemini
;; env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_network_esearch
;; env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_local_xfetch -v
;; env EDIRECT_LOCAL_ARCHIVE=/export3/PubMed/Source python3 -m unittest tests.test_network_gemini_ontology
;;
;; Note: API key is read from ~/.config/gemini/credentials
;;
(define-module (guix)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system gnu)
#: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 bash)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages wget)
#:use-module (gnu packages gawk)
#:use-module (gnu packages golang)
#:use-module (gnu packages golang-build)
#:use-module (gnu packages golang-compression)
#:use-module (gnu packages golang-xyz)
#: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 nss)
#:use-module (gnu packages perl)
#:use-module (gnu packages xml)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gn packages javascript)
#:use-module (gn packages web))
(define %source-dir (dirname (current-filename)))
(define nltk-punkt-source
(origin
(method url-fetch)
(uri "https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt_tab.zip")
(sha256
(base32 "01h11srafj57yvp74xkidikh6m7ch7qscz21lck7f9vlg4c68zz5"))))
(define-public nltk-punkt
(package
(name "nltk-punkt")
(version "1.0")
(source nltk-punkt-source)
(build-system gnu-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(delete 'check)
(replace 'unpack
(lambda* (#:key source #:allow-other-keys)
(invoke "unzip" source)))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (string-append (assoc-ref outputs "out")
"/share/nltk_data/tokenizers/punkt_tab")))
(mkdir-p out)
(copy-recursively "punkt_tab" out)))))))
(native-inputs (list unzip))
(home-page "https://www.nltk.org/nltk_data/")
(synopsis "NLTK Punkt_Tab sentence tokenizer models")
(description "Pre-trained models for the Punkt sentence boundary
detection tokenizer (tab format), used by NLTK's sent_tokenize function.")
(license license:asl2.0)))
(define minipubmed-source
(origin
(method url-fetch)
(uri "https://git.genenetwork.org/genecup/plain/minipubmed.tgz")
(sha256
(base32 "116k7plhn7xkbv170035si7xhbfqb1ff15rxqwimjrwm8rb1bbcc"))))
(define-public minipubmed
(package
(name "minipubmed")
(version "1.0")
(source minipubmed-source)
(build-system gnu-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(delete 'check)
(replace 'unpack
(lambda* (#:key source #:allow-other-keys)
(invoke "tar" "xzf" source)))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (string-append (assoc-ref outputs "out")
"/share/minipubmed")))
;; Generate test.xml from pmid.list
(with-directory-excursion "minipubmed"
;; Generate test.xml from pmid.list using xfetch
(system "cat pmid.list | xfetch -db pubmed > test.xml"))
(mkdir-p out)
(copy-recursively "minipubmed" out)))))))
(inputs (list edirect-25))
(home-page "https://genecup.org")
(synopsis "Mini PubMed archive for GeneCup testing")
(description "A small collection of 2473 PubMed abstracts for testing
GeneCup with four gene symbols (gria1, crhr1, drd2, and penk).")
(license license:expat)))
(define-public edirect-25
(package
(name "edirect-25")
(version "25.2.20260328")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
"/versions/" version
"/edirect-" version ".tar.gz"))
(sha256
(base32 "04km4hrnmiganafwn5516hm8n0var9ilhbr068chy8v95xk131x6"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file "Mozilla-CA.tar.gz")
(delete-file "cacert.pem")))
(patches
(list (local-file "contrib/patches/edirect-xml-bounds-check.patch")))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #t
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'patch-path-reset
(lambda _
;; These scripts reset PATH=/bin:/usr/bin which breaks Guix
(substitute* '("xtract" "rchive" "transmute")
(("PATH=/bin:/usr/bin")
"PATH=\"/bin:/usr/bin:$PATH\""))))
(add-after 'unpack 'patch-go-version
(lambda _
;; Relax Go version requirement to match available toolchain
(substitute* '("cmd/go.mod" "eutils/go.mod")
(("go 1\\.26\\.1") "go 1.26.0"))))
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(setenv "HOME" (getcwd))
(setenv "GOTOOLCHAIN" "local")
(setenv "GO111MODULE" "off")
;; Build GOPATH from Guix Go package inputs + local eutils
(let ((gopath (string-append (getcwd) "/gopath")))
(mkdir-p (string-append gopath "/src"))
(symlink (string-append (getcwd) "/eutils")
(string-append gopath "/src/eutils"))
(setenv "GOPATH"
(string-join
(cons gopath
(map cdr
(filter
(lambda (input)
(directory-exists?
(string-append (cdr input) "/src")))
inputs)))
":")))
(with-directory-excursion "cmd"
(for-each
(lambda (prog)
(invoke "go" "build" "-v"
"-o" (string-append prog ".Linux")
(string-append prog ".go")))
'("xtract" "rchive" "transmute")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
;; Install Go binaries
(for-each
(lambda (prog)
(install-file (string-append "cmd/" prog ".Linux") bin))
'("xtract" "rchive" "transmute"))
;; Install executable scripts
(for-each
(lambda (f)
(when (and (not (file-is-directory? f))
(access? f X_OK)
(not (string-suffix? ".go" f))
(not (string-suffix? ".py" f))
(not (string-suffix? ".pm" f))
(not (string-suffix? ".pdf" f))
(not (string-suffix? ".pem" f))
(not (string-suffix? ".gz" f))
(not (member (basename f)
'("LICENSE" "README"))))
(install-file f bin)))
(find-files "."
(lambda (f s)
(and (not (string-contains f "/cmd/"))
(not (string-contains f "/eutils/"))
(not (string-contains f "/gopath/"))))
#:directories? #f))
;; Install extern/ data (contains .ini config files)
(copy-recursively "extern"
(string-append bin "/extern")))))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(coreutils (assoc-ref inputs "coreutils")))
;; Only wrap scripts directly in bin/, not in
;; subdirs (extern/ scripts are sourced, not executed).
;; Skip .sh (sourced) and .Linux (Go binaries).
(for-each
(lambda (f)
(wrap-program f
`("PATH" ":" prefix
(,bin ,(string-append coreutils "/bin")))))
(filter
(lambda (f)
(and (string=? (dirname f) bin)
(not (string-suffix? ".sh" f))
(not (string-suffix? ".Linux" f))))
(find-files bin)))
;; wrap-program renames xtract -> .xtract-real, but the
;; script looks for $0.Linux, so create symlinks
(for-each
(lambda (prog)
(symlink (string-append bin "/" prog ".Linux")
(string-append bin "/." prog "-real.Linux")))
'("xtract" "rchive" "transmute")))))
(delete 'check)
(add-after 'wrap-programs 'smoke-test
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
;; Smoke test: xtract.Linux parses XML
(invoke "sh" "-c"
(string-append
"echo '<test><a>hello</a><b>world</b></test>' | "
bin "/xtract.Linux -pattern test -element a b"
" | grep -q hello"))
;; Smoke test: rchive.Linux version
(invoke (string-append bin "/rchive.Linux") "-version")
;; Smoke test: transmute.Linux version
(invoke (string-append bin "/transmute.Linux")
"-version")))))))
(native-inputs
(list go-1.26
go-github-com-fatih-color
go-github-com-gedex-inflector
go-github-com-goccy-go-yaml
go-github-com-klauspost-compress
go-github-com-klauspost-cpuid-v2
go-github-com-klauspost-pgzip
go-github-com-komkom-toml
go-github-com-mattn-go-colorable
go-github-com-mattn-go-isatty
go-github-com-pbnjay-memory
go-github-com-pkg-errors
go-github-com-surgebase-porter2
go-golang-org-x-sys
go-golang-org-x-text))
(propagated-inputs (list curl wget grep sed gawk coreutils findutils gzip unzip findutils))
(inputs (list bash-minimal coreutils perl perl-xml-simple python))
(home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases")
(description "Entrez Direct (EDirect) provides access to the NCBI's suite
of interconnected databases from a Unix terminal window. Search terms are
entered as command-line arguments. Individual operations are connected with
Unix pipes to construct multi-step queries. Selected records can then be
retrieved in a variety of formats.")
(license license:public-domain)))
(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
python-google-auth
python-httpx
python-pydantic
python-requests
python-tenacity
python-websockets
python-typing-extensions
python-distro
python-sniffio
sed))
(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-gemini
(package
(name "genecup-gemini")
(version "1.9")
(source (local-file %source-dir #:recursive? #t))
(build-system python-build-system)
(arguments
(list
#:tests? #t
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(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 'setup-minipubmed
(lambda* (#:key inputs #:allow-other-keys)
(delete-file "minipubmed.tgz")
(let ((pubmed (string-append (assoc-ref inputs "minipubmed")
"/share/minipubmed/PubMed")))
;; Patch default pubmed path to store location
(substitute* "more_functions.py"
(("\\./minipubmed") pubmed)))))
(replace 'check
(lambda _
;; test_network_* files need internet, skip them
(invoke "python" "-m" "unittest" "tests.test_hello" "-v")))
(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 'create-bin-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "GUIX_PYTHONPATH")))
(mkdir-p (string-append out "/bin"))
(call-with-output-file (string-append out "/bin/genecup")
(lambda (port)
(format port "#!~a~%cd ~a~%exec ~a/server.py \"$@\"~%"
(which "bash") out out)))
(chmod (string-append out "/bin/genecup") #o755)
(wrap-program (string-append out "/bin/genecup")
`("PATH" ":" prefix (,(dirname (which "esearch"))
,(dirname (which "dirname"))
,(dirname (which "grep"))
,(dirname (which "sed"))))
`("GUIX_PYTHONPATH" ":" prefix (,path))
`("NLTK_DATA" ":" prefix
(,(string-append (assoc-ref inputs "nltk-punkt")
"/share/nltk_data"))))))))))
(propagated-inputs
(list
curl
findutils
python-bcrypt
python-flask
python-flask-sqlalchemy
python-google-genai
python-nltk
python-pandas
python-pytz
python
nss-certs
openssl
))
(inputs
`(("edirect-25" ,edirect-25)
("inetutils" ,inetutils)
("gzip" ,gzip)
("minipubmed" ,minipubmed)
("tar" ,tar)
;; 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)
("nltk-punkt" ,nltk-punkt)
("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-gemini
