diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 192 |
1 files changed, 192 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35b0cef0bd..59128dcba1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1062,6 +1062,198 @@ simultaneously considered.") with DNA methylation micro-array data.") (license license:unlicense)))) +(define-public r-hdwgcna + (let ((commit "950b8c74c5d74b30b4a562820e70ca00ee29e2c6") + (revision "1")) + (package + (name "r-hdwgcna") + (version (git-version "0.4.00" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smorabit/hdWGCNA") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0d9hr2ly7k6kq6yp5spjlp6lp9yx593xmggajyzjxlhxi2lbyqgn")) + (snippet + '(for-each delete-file + (list + "docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js" + "docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js" + "docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js" + "docs/deps/clipboard.js-2.0.11/clipboard.min.js" + "docs/deps/headroom-0.11.0/headroom.min.js" + "docs/deps/headroom-0.11.0/jQuery.headroom.min.js" + "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js" + "docs/deps/search-1.0.0/autocomplete.jquery.min.js" + "docs/deps/search-1.0.0/fuse.min.js" + "docs/deps/search-1.0.0/mark.min.js"))))) + (properties `((upstream-name . "hdWGCNA"))) + (build-system r-build-system) + (arguments + (list + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules (guix build minify-build-system)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "docs/deps/" + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(string-append (assoc-ref inputs "js-bootstrap-5.1") + "/dist/js/bootstrap.bundle.js") + . "bootstrap-5.1.0/bootstrap.bundle.min.js") + (,(string-append (assoc-ref inputs "js-bootstrap-5.3") + "/dist/js/bootstrap.bundle.js") + . "bootstrap-5.3.1/bootstrap.bundle.min.js") + (,(search-input-file inputs "/dist/bootstrap-toc.js") + . "bootstrap-toc-1.0.1/bootstrap-toc.min.js") + (,(search-input-file inputs "/dist/clipboard.js") + . "clipboard.js-2.0.11/clipboard.min.js") + ("jquery-3.6.0/jquery-3.6.0.js" + . "jquery-3.6.0/jquery-3.6.0.min.js") + (,(search-input-file inputs "/dist/autocomplete.jquery.js") + . "search-1.0.0/autocomplete.jquery.min.js") + (,(search-input-file inputs "/dist/fuse.js") + . "search-1.0.0/fuse.min.js") + (,(search-input-file inputs "/dist/mark.js") + . "search-1.0.0/mark.min.js") + (,(assoc-ref inputs "js-headroom") + . "headroom-0.11.0/headroom.min.js") + (,(assoc-ref inputs "js-headroom-jquery") + . "docs/deps/headroom-0.11.0/jQuery.headroom.min.js"))))))))) + (propagated-inputs (list r-dplyr + r-enrichr + r-geneoverlap + r-genomicranges + r-ggplot2 + r-ggraph + r-ggrepel + r-harmony + r-igraph + r-matrix + r-proxy + r-seurat + r-tester + r-tidygraph + r-ucell + r-wgcna)) + (native-inputs + `(("esbuild" ,esbuild) + ("js-autocomplete" + ,(let ((version "0.38.0")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/algolia/autocomplete") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-autocomplete" version)) + (sha256 + (base32 + "04r1qmd5cxcf8cf471kx51y6wq86rh54y42y7xl51z95ag5csswl"))))) + ("js-bootstrap-5.1" + ,(let ((version "5.1.0")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/twbs/bootstrap") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-bootstrap" version)) + (sha256 + (base32 + "0wjyi497wy2lbypkxwa72z294zbh827lb2s8pzgi40hvjsw00ns4"))))) + ("js-bootstrap-5.3" + ,(let ((version "5.3.1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/twbs/bootstrap") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-bootstrap" version)) + (sha256 + (base32 + "045majqayd4wrpq3r3fisi56grwizykwj5705jlzsg7bwln8v3qr"))))) + ("js-bootstrap-toc" + ,(let ((version "1.0.1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/afeld/bootstrap-toc") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-bootstrap-toc" version)) + (sha256 + (base32 + "1d4rqvbkwmmld0d8nz2is1rwc55rlb4b0v2anylxj63335cs0mk0"))))) + ("js-clipboard" + ,(let ((version "2.0.11")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/zenorocha/clipboard.js") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-clipboard" version)) + (sha256 + (base32 + "0nn9cry7ddf47vkl3vnpc4z86da46wq7m3qf3awcs05197bjn1vj"))))) + ("js-fuse" + ,(let ((version "6.4.6")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/krisk/Fuse") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-fuse" version)) + (sha256 + (base32 + "1k0l2vxw4nsmwrz48kmgv41ymphrdwbdbckiv9w011jwbnfsqvn5"))))) + ("js-mark" + ,(let ((version "8.11.1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/julkue/mark.js") + (commit version))) + (file-name (git-file-name "js-mark" version)) + (sha256 + (base32 + "108cw4732wjlwwjwpc86fqlr8yfrlagqdn7126qxa70c0ldfma93"))))) + ("js-headroom" + ,(let ((version "0.11.0")) + (origin + (method url-fetch) + (uri (string-append "https://unpkg.com/headroom.js@" + version "/dist/headroom.js")) + (file-name (string-append "js-headroom-" version ".js")) + (sha256 + (base32 + "0d76fpajxzwsj4847zgrv05daq8ri8hcww5dcldq1q2iyyxsmrva"))))) + ("js-headroom-jquery" + ,(let ((version "0.11.0")) + (origin + (method url-fetch) + (uri (string-append "https://unpkg.com/headroom.js@" + version "/dist/jQuery.headroom.js")) + (file-name (string-append "js-headroom-jquery-" version ".js")) + (sha256 + (base32 + "1jz1ampd9k8p32m6bid4yrr66bkngd8blj2q0774hl91rszhjqrv"))))))) + (home-page "https://github.com/smorabit/hdWGCNA") + (synopsis "Weighted gene co-expression network analysis") + (description + "@code{hdWGCNA} is an R package for performing weighted gene +co-expression network analysis in high dimensional -omics such as single-cell +RNA-seq or spatial transcriptomics.") + (license license:gpl3)))) + (define-public r-netid (let ((commit "6ad1ffdd64a6584cc1d392524dad8e248d4590a8") (revision "1")) |