diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 7 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 94 | ||||
| -rw-r--r-- | gn/packages/ratspub.scm | 134 |
3 files changed, 77 insertions, 158 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 1539919..8897752 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -483,16 +483,15 @@ reads.") "/xtract.Linux")) ;; March 10, 2016 (sha256 (base32 - "0wppi3q3wcind6za043w0g7a987qr59yiyh553h46a1apjkd8y9b")))) + "15yhhh8kfipk12rhzabap81ys8wgj0khn0mp8p7zwqhq028fwj0l")))) ("rchive.Linux" ,(origin (method url-fetch) (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "versions/" (package-version edirect) "/rchive.Linux")) - (file-name (string-append "rchive.Linux-" (package-version edirect))) + "/rchive.Linux")) ;; November 14, 2017 (sha256 (base32 - "134y0zprplqlplc6qmcjb97411bxkwghmq3z0qjgh0dgdbzjq1w3")))))) + "0hl8zj1md9xbmaj0pv99rjyisw8w74rirw97xwqk47dz8v8ml338")))))) (native-search-paths ;; Ideally this should be set for LWP somewhere. (list (search-path-specification diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index c9c7a87..f8c2cba 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -9,35 +9,6 @@ ;; Please keep these packages sorted alphabetically -(define-public rust-itertools-0.7 - (package - (name "rust-itertools") - (version "0.7.11") - (source - (origin - (method url-fetch) - (uri (crate-uri "itertools" version)) - (file-name (string-append name "-" version ".crate")) - (sha256 - (base32 - "03cpsj26xmyamcalclqzr1i700vwx8hnbgxbpjvs354f8mnr8iqd")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-either" ,rust-either-1.5)) - #:cargo-development-inputs - (("rust-permutohedron" ,rust-permutohedron-0.2) - ("rust-quickcheck" ,rust-quickcheck-0.5)))) - (home-page "https://github.com/rust-itertools/itertools") - (synopsis - "Extra iterator adaptors, iterator methods, free functions, and macros") - (description - "Extra iterator adaptors, iterator methods, free functions, and macros.") - (properties '((hidden? . #t))) - (license (list license:asl2.0 - license:expat)))) - (define-public rust-ndarray-0.12 (package (name "rust-ndarray") @@ -58,7 +29,7 @@ ("rust-matrixmultiply" ,rust-matrixmultiply-0.1) ("rust-num-complex" ,rust-num-complex-0.2) ;("rust-blas-src" ,rust-blas-src-0.2) - ;("rust-cblas-src" ,rust-cblas-src-0.1) + ("rust-cblas-sys" ,rust-cblas-sys-0.1) ("rust-rustc-serialize" ,rust-rustc-serialize-0.3) ("rust-serde" ,rust-serde-1.0)) #:cargo-development-inputs @@ -66,65 +37,8 @@ ("rust-quickcheck" ,rust-quickcheck-0.7) ("rust-rawpointer" ,rust-rawpointer-0.1)))) (home-page "https://github.com/rust-ndarray/ndarray") - (synopsis - "ndarray implements an n-dimensional container for general elements and for numerics") - (description - "ndarray implements an n-dimensional container for general elements and for numerics.") - (properties '((hidden? . #t))) - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-structopt-0.2 - (package - (name "rust-structopt") - (version "0.2.18") - (source - (origin - (method url-fetch) - (uri (crate-uri "structopt" version)) - (file-name (string-append name "-" version ".crate")) - (sha256 - (base32 - "1mvfv1l8vp3y402fkl2wcl34hi7gmr4bqha13dfz2xf3kjzwvhhn")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-clap" ,rust-clap-2) - ("rust-structopt-derive" ,rust-structopt-derive-0.2)))) - (home-page "https://github.com/TeXitoi/structopt") - (synopsis "Parse command line arguments by defining a struct") - (description - "Parse command line arguments by defining a struct.") - (properties '((hidden? . #t))) - (license (list license:asl2.0 - license:expat)))) - -(define-public rust-structopt-derive-0.2 - (package - (name "rust-structopt-derive") - (version "0.2.18") - (source - (origin - (method url-fetch) - (uri (crate-uri "structopt-derive" version)) - (file-name (string-append name "-" version ".crate")) - (sha256 - (base32 - "01sis9z5kqmyhvzbnmlzpdxcry99a0b9blypksgnhdsbm1hh40ak")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t - #:cargo-inputs - (("rust-heck" ,rust-heck-0.3) - ("rust-proc-macro2" ,rust-proc-macro2-0.4) - ("rust-quote" ,rust-quote-0.6) - ("rust-syn" ,rust-syn-0.15)))) - (home-page "https://github.com/TeXitoi/structopt") - (synopsis - "Parse command line argument by defining a struct, derive crate") - (description - "Parse command line argument by defining a struct, derive crate.") - (properties '((hidden? . #t))) + (synopsis "n-dimensional container for general elements and for numerics") + (description "@code{ndarray} implements an n-dimensional container for +general elements and for numerics.") (license (list license:asl2.0 license:expat)))) diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm index da6df5f..29e1313 100644 --- a/gn/packages/ratspub.scm +++ b/gn/packages/ratspub.scm @@ -11,73 +11,79 @@ #:use-module (gn packages web)) (define-public ratspub - (let ((commit "88ab6a3a21fcc2715c9a7528d8b4d15bb7ea85ed") - (revision "2")) - (package - (name "ratspub") - (version (git-version "0.0.0" revision commit)) ; Aug 30, 2019 - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/chen42/ratspub.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0gg2wikajbz248qgg7vyclrmjhdw01wb721zvzgil9qd2gm0g4c6")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; no test suite - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (add-after 'unpack 'patch-sources - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (cytoscape (assoc-ref inputs "cytoscape")) - (bootstrap (assoc-ref inputs "bootstrap")) - (inetutils (assoc-ref inputs "inetutils"))) - ;; Source cannot find the substituted css currently. - ;(substitute* "templates/cytoscape.html" - ; (("script src=.*") - ; (string-append "script src=\"" cytoscape - ; "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js\"></script>\n"))) - ;(substitute* "templates/layout.html" - ; (("https://stackpath.bootstrapcdn.com/bootstrap/.*") - ; (string-append bootstrap "/share/web/bootstrap/css/bootstrap.min.css\">\n"))) - (substitute* "ratspub.py" - (("hostname") (string-append inetutils "/bin/hostname")))) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (copy-recursively "." out)) - #t)) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (path (getenv "PYTHONPATH"))) - (wrap-program (string-append out "/server.py") - `("PATH" ":" prefix (,(dirname (which "edirect.pl")))) - `("PYTHONPATH" ":" prefix (,path)))) - #t))))) - (inputs - `(("edirect" ,edirect-gn) - ("inetutils" ,inetutils) - ("python-flask" ,python-flask) - ("python-nltk" ,python-nltk))) - (native-inputs - `(("cytoscape" ,javascript-cytoscape) - ("bootstrap" ,web-bootstrap))) - (home-page "http://rats.pub/") - (synopsis "Relationship with Addiction Through Searches of PubMed") - (description - "RatsPub searches PubMed to find sentences that contain the query terms + (package + (name "ratspub") + (version "0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chen42/ratspub.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cm9g38fxpa52458mdmhzhghj5c7b8l3k1b764zs9hdrki5s7wi7")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; no test suite + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (add-after 'unpack 'patch-sources + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (inetutils (assoc-ref inputs "inetutils"))) + (substitute* "templates/cytoscape.html" + (("script src=.*") + "script src=\"/static/cytoscape.min.js\"></script>\n")) + (substitute* "templates/layout.html" + (("https://stackpath.bootstrapcdn.com/bootstrap/.*") + "/static/bootstrap.min.css\">\n")) + (substitute* "ratspub.py" + (("hostname") (string-append inetutils "/bin/hostname")))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (copy-recursively "." out)) + #t)) + (add-after 'install 'install-javascript + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (cytoscape (assoc-ref inputs "cytoscape")) + (bootstrap (assoc-ref inputs "bootstrap"))) + (symlink (string-append cytoscape + "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js") + (string-append out "/static/cytoscape.min.js")) + (symlink (string-append bootstrap + "/share/web/bootstrap/css/bootstrap.min.css") + (string-append out "/static/bootstrap.min.css"))) + #t)) + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out "/server.py") + `("PATH" ":" prefix (,(dirname (which "edirect.pl")))) + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("edirect" ,edirect-gn) + ("inetutils" ,inetutils) + ("python-flask" ,python-flask) + ("python-nltk" ,python-nltk))) + (native-inputs + `(("cytoscape" ,javascript-cytoscape) + ("bootstrap" ,web-bootstrap))) + (home-page "http://rats.pub/") + (synopsis "Relationship with Addiction Through Searches of PubMed") + (description + "RatsPub searches PubMed to find sentences that contain the query terms (i.e., gene symbols) and drug addiction-related keywords. These gene-keyword relationships are presented as an interactive graph that can efficiently answer the question \"What do we know about these genes and addiction?\". Data from @acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association Studies} catalog are also included in the search to better answer this question.") - (license #f)))) + (license #f))) |