Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

1 files changed, 132 insertions, 0 deletions

diff --git a/gn/packages/maths.scm b/gn/packages/maths.scm
new file mode 100644
index 0000000..320d83c
--- /dev/null
+++ b/gn/packages/maths.scm
@@ -0,0 +1,132 @@
+(define-module (gn packages maths)
+  #:use-module (gnu packages)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (gnu packages gperf)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages texinfo)
+  #:use-module (srfi srfi-1))
+
+(define-public octave-3.4.3
+  (package
+    (inherit octave-cli)
+    (name "octave")
+    (version "3.4.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://gnu/octave/octave-"
+                            version ".tar.gz"))
+        (sha256
+         (base32
+          "04lh3crzwpramvfvxq34n2r29pmfl37rssj853nz9a3pyq7wrrir"))
+        (patches (search-patches "gnulib-gets.patch"
+                                 "octave-nested-class.patch"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments octave-cli)
+       ((#:configure-flags cf)
+        `(cons "--enable-docs=no" ; docs fail to build
+               ,cf))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'patch-configure-script
+             (lambda _
+               (substitute* '("configure"
+                              "src/DLD-FUNCTIONS/__delaunayn__.cc"
+                              "src/DLD-FUNCTIONS/__voronoi__.cc"
+                              "src/DLD-FUNCTIONS/convhulln.cc")
+                 (("qhull/qhull.h") "libqhull/libqhull.h")
+                 (("qhull/qhull_a.h") "libqhull/qhull_a.h"))
+               (copy-file (assoc-ref %build-inputs "fseeko.c")
+                          "libgnu/fseeko.c")
+               #t))
+           (replace 'configure-makeinfo
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "src/help.cc"
+                 (("\"makeinfo\"")
+                  (string-append
+                    "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
+               #t))))))
+    (native-inputs
+     `(("fseeko.c" ,(origin
+                      (method url-fetch)
+                      (uri "https://git.savannah.gnu.org/gitweb/?p=gnulib.git;a=blob_plain;f=lib/fseeko.c;hb=d40db5e23197dcd105fa3c0dc6633b51af3c08d9")
+                      (file-name "gnulib-fseeko.c-0.0.0-1-d40db5e23")
+                      (sha256
+                       (base32
+                        "1ifa5200pskgdzd6qi4nicwyjjkc415bs403mjrrzv8cdrf6hp3k"))))
+       ,@(fold alist-delete (package-native-inputs octave-cli)
+               '("lzip"))))
+    (inputs
+     `(("glpk" ,glpk-4.48)
+       ("gperf" ,gperf)
+       ,@(fold alist-delete (package-inputs octave-cli)
+               ;; suitesparse provides cholmod_common_struct, may need older version
+               '("glpk" "suitesparse"))))))
+
+;; 4.49 is the last version with _glp_lpx_simplex exported
+;; 4.49 is the version where all lpx_ routines were removed
+(define-public glpk-4.48
+  (package
+    (inherit glpk)
+    (version "4.48")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "mirror://gnu/glpk/glpk-"
+                          version ".tar.gz"))
+      (sha256
+       (base32
+        "1cddqsdcfwavdklg7hsfifppsry81dx3c17wzk6r22mjjpwcihmb"))))))
+
+(define-public suitesparse-3.5.0
+  (package
+    (inherit suitesparse)
+    (version "3.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0npn7c1j5qag5m2r0cmh3bwc42c1jk8k2yg2cfyxlcrp0h7wn4rc"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments suitesparse)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'unpack-metis
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((metis (assoc-ref inputs "metis-source")))
+                 (invoke "tar" "xvf" metis)
+                 ;; backported from 4.0.3
+                 (substitute* (find-files "metis-4.0")
+                              (("log2") "ilog2")))
+               #t))
+           (add-after 'unpack 'fix-source
+             (lambda _
+               (substitute* "UFconfig/Makefile"
+                 (("Lib/") ""))
+               ;; octave-3.4.3 expects it to be built with -fPIC
+               (substitute* "UFconfig/UFconfig.mk"
+                 (("-O3") "-O3 -fPIC"))
+               #t))
+           (add-before 'install 'prepare-directories
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (mkdir-p (string-append out "/lib"))
+                 (mkdir-p (string-append out "/include")))
+               #t))))))
+    (native-inputs
+     `(("metis-source" ,(origin
+                          (method url-fetch)
+                          (uri "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.1.tar.gz")
+                          (sha256
+                           (base32
+                            "0lnkdfdrmmyy67h356bgdc06acvmcr26av9kdvqlws12znrr5iv0"))))
+       ,@(package-native-inputs suitesparse)))
+    (inputs
+     `(,@(fold alist-delete (package-inputs suitesparse)
+               '("metis"))))))