Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics

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)))