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authorpjotrp2020-02-10 12:26:32 -0600
committerpjotrp2020-02-10 12:26:32 -0600
commiteb94413a21c656e0bf344145cbf901b1e7fea15c (patch)
treee84caf3e0eca92f20d9b80f060cb5e445ef28943 /gn
parentdb77e0f800f513185e76aa770c670e6fbfdf791b (diff)
parentf59968258e8fc258601f4ebddd4aef44900584a9 (diff)
downloadguix-bioinformatics-eb94413a21c656e0bf344145cbf901b1e7fea15c.tar.gz
Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm7
-rw-r--r--gn/packages/crates-io.scm94
-rw-r--r--gn/packages/ratspub.scm134
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)))