diff options
| -rw-r--r-- | README.md | 29 | ||||
| -rw-r--r-- | etc/archive-pubmed.service | 15 | ||||
| -rw-r--r-- | guix.scm | 138 |
3 files changed, 166 insertions, 16 deletions
diff --git a/README.md b/README.md index 7c09004..0df4841 100644 --- a/README.md +++ b/README.md @@ -35,16 +35,6 @@ You can use the [guix.scm](./guix.scm) container to run genecup: Note that the build includes minipubmed and punkt for testing! -## Gemini API credentials - -For stress classification via Gemini, create a credentials file: - -```sh -mkdir -p ~/.config/gemini -echo "YOUR_API_KEY_HERE" > ~/.config/gemini/credentials -``` - -The server reads the API key from `~/.config/gemini/credentials` on startup. # Run a production server @@ -73,6 +63,17 @@ NLTK_DATA: punkt_tab directory (defaults to built-in nltk-punkt) TMPDIR (default /tmp) ``` +## Gemini API credentials + +For stress classification via Gemini, create a credentials file: + +```sh +mkdir -p ~/.config/gemini +echo "YOUR_API_KEY_HERE" > ~/.config/gemini/credentials +``` + +The server reads the API key from `~/.config/gemini/credentials` on startup. + # Development @@ -99,7 +100,7 @@ You also need to fetch punkt.zip from https://www.nltk.org/nltk_data/ cd minipubmed mkdir tokenizers cd tokenizers -wget https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt.zip +wget https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt_tab.zip unzip punkt.zip ``` @@ -107,15 +108,15 @@ unzip punkt.zip The source code and data are in a git repository: https://git.genenetwork.org/genecup/ -## Support +# Support E-mail [Pjotr Prins](https://thebird.nl) or [Hao Chen](https://www.uthsc.edu/neuroscience-institute/about/faculty/chen.php). -## License +# License GeneCup source code is published under the liberal free software MIT licence (aka expat license) -## Cite +# Cite [GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships](https://academic.oup.com/g3journal/article/12/5/jkac059/6548160) by Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, and Chen H. diff --git a/etc/archive-pubmed.service b/etc/archive-pubmed.service new file mode 100644 index 0000000..ba5b293 --- /dev/null +++ b/etc/archive-pubmed.service @@ -0,0 +1,15 @@ +# Example of a systemd service to update the PubMed archive (with indexing) +[Unit] +Description=Download PubMed Archives +After=network-online.target +Wants=network-online.target +AssertPathExists=/export/PubMed + +[Service] +ExecStart=/usr/local/guix-profiles/genecup/bin/index-pubmed +Environment="EDIRECT_PUBMED_MASTER=/export/PubMed" "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt" "PATH=/usr/local/guix-profiles/ratspub/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin:/usr/sbin" +User=hchen + +[Install] +WantedBy=multi-user.target + diff --git a/guix.scm b/guix.scm index 0dc9b76..580afc2 100644 --- a/guix.scm +++ b/guix.scm @@ -24,8 +24,12 @@ #:use-module (guix utils) #:use-module (gnu packages admin) #:use-module (gnu packages base) - #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages bash) #:use-module (gnu packages compression) + #: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) @@ -35,6 +39,8 @@ #: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) @@ -117,6 +123,134 @@ detection tokenizer (tab format), used by NLTK's sent_tokenize function.") GeneCup with four gene symbols (gria1, crhr1, drd2, and penk).") (license license:expat))) +(define-public edirect + (package + (name "edirect") + (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"))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; tests require network access to NCBI servers + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (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))))) + (add-after 'install 'wrap-programs + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + ;; Don't wrap .sh files -- they are sourced, not executed + (for-each + (lambda (f) + (wrap-program f `("PATH" ":" prefix (,bin)))) + (filter + (lambda (f) (not (string-suffix? ".sh" 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")))))))) + (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)) + (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") @@ -238,7 +372,7 @@ access to Gemini models.") (which "bash") out out))) (chmod (string-append out "/bin/genecup") #o755) (wrap-program (string-append out "/bin/genecup") - `("PATH" ":" prefix (,(dirname (which "edirect.pl")) + `("PATH" ":" prefix (,(dirname (which "esearch")) ,(dirname (which "dirname")) ,(dirname (which "grep")) ,(dirname (which "sed")))) |