gnu: Separate Python core packages from the rest.

[jackhill/guix/guix.git] / gnu / packages / machine-learning.scm

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 7b9b28a..b56468f 100644 (file)
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -54,6 +55,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages xml)
@@ -331,8 +333,8 @@ algorithm.")
      (origin
        (method url-fetch)
        (uri (string-append
-             "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
-             "randomjungle-" version ".tar_.gz"))
+             "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
+             "/randomjungle/randomjungle-" version ".tar_.gz"))
        (patches (search-patches "randomjungle-disable-static-build.patch"))
        (sha256
         (base32
@@ -361,7 +363,7 @@ algorithm.")
     ;; Non-portable assembly instructions are used so building fails on
     ;; platforms other than x86_64 or i686.
     (supported-systems '("x86_64-linux" "i686-linux"))
-    (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
+    (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
     (synopsis "Implementation of the Random Forests machine learning method")
     (description
      "Random Jungle is an implementation of Random Forests.  It is supposed to
@@ -494,7 +496,7 @@ sample proximities between pairs of cases.")
      `(("python" ,python)
        ("numpy" ,python-numpy)
        ("r-minimal" ,r-minimal)
-       ("octave" ,octave)
+       ("octave" ,octave-cli)
        ("swig" ,swig)
        ("eigen" ,eigen)
        ("hdf5" ,hdf5)
@@ -718,7 +720,7 @@ computing environments.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0qv7ir1fy9vjar3llc72yxmfja3gxm5icdf0y3q57vsn3wcdglkz"))))
+         "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -872,3 +874,37 @@ the following advantages:
 such as online, hashing, allreduce, reductions, learning2search, active, and
 interactive learning.")
     (license license:bsd-3)))
+
+(define-public python2-fastlmm
+  (package
+    (name "python2-fastlmm")
+    (version "0.2.21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "fastlmm" version ".zip"))
+       (sha256
+        (base32
+         "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2)) ; only Python 2.7 is supported
+    (propagated-inputs
+     `(("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-matplotlib" ,python2-matplotlib)
+       ("python2-pandas" ,python2-pandas)
+       ("python2-scikit-learn" ,python2-scikit-learn)
+       ("python2-pysnptools" ,python2-pysnptools)))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("python2-cython" ,python2-cython)
+       ("python2-mock" ,python2-mock)
+       ("python2-nose" ,python2-nose)))
+    (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
+    (synopsis "Perform genome-wide association studies on large data sets")
+    (description
+     "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
+Models, is a program for performing both single-SNP and SNP-set genome-wide
+association studies (GWAS) on extremely large data sets.")
+    (license license:asl2.0)))