Merge branch 'master' into staging

[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b051389..1a82815 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
-;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
@@ -66,6 +66,8 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages code)
+  #:use-module (gnu packages commencement)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages cran)
@@ -82,6 +84,7 @@
   #:use-module (gnu packages golang)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graph)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages gtk)
@@ -91,6 +94,7 @@
   #:use-module (gnu packages haskell-web)
   #:use-module (gnu packages haskell-xyz)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages image-processing)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
   #:use-module (gnu packages java-compression)
@@ -11169,23 +11173,44 @@ programs for inferring phylogenies (evolutionary trees).")
          "1z1vcpwbylixk0zywngg5iw0jv083jj1bqphi817jpg3fb9fx2jj"))))
     (build-system cmake-build-system)
     (arguments
-     `(;; FIXME: Some tests fail because they produce warnings, others fail
-       ;; because the PYTHONPATH does not include the modeller's directory.
-       #:tests? #f))
+     `( ;; CMake 3.17 or newer is required for the CMAKE_TEST_ARGUMENTS used
+       ;; below to have an effect.
+       #:cmake ,cmake
+       #:configure-flags
+       (let ((disabled-tests
+              '("expensive"                 ;exclude expensive tests
+                "IMP.modeller"              ;fail to import its own modules
+                "IMP.parallel-test_sge.py"  ;fail in build container
+                ;; The following test fails non-reproducibly on
+                ;; an inexact numbers assertion.
+                "IMP.em-medium_test_local_fitting.py")))
+         (list
+          (string-append
+           "-DCMAKE_CTEST_ARGUMENTS="
+           (string-join
+            (list "-L" "-tests?-"       ;select only tests
+                  "-E" (format #f "'(~a)'" (string-join disabled-tests "|")))
+            ";"))))))
+    (native-inputs
+     `(("python" ,python-wrapper)
+       ("swig" ,swig)))
     (inputs
      `(("boost" ,boost)
+       ("cgal" ,cgal)
        ("gsl" ,gsl)
-       ("swig" ,swig)
        ("hdf5" ,hdf5)
        ("fftw" ,fftw)
        ("eigen" ,eigen)
-       ("python" ,python-2)))
+       ;; Enabling MPI causes the build to use all the available memory and
+       ;; fail (tested on a machine with 32 GiB of RAM).
+       ;;("mpi" ,openmpi)
+       ("opencv" ,opencv)))
     (propagated-inputs
-     `(("python2-numpy" ,python2-numpy)
-       ("python2-scipy" ,python2-scipy)
-       ("python2-pandas" ,python2-pandas)
-       ("python2-scikit-learn" ,python2-scikit-learn)
-       ("python2-networkx" ,python2-networkx)))
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-pandas" ,python-pandas)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-networkx" ,python-networkx)))
     (home-page "https://integrativemodeling.org")
     (synopsis "Integrative modeling platform")
     (description "IMP's broad goal is to contribute to a comprehensive
@@ -11203,7 +11228,7 @@ applications for tackling some common problems in a user-friendly way.")
 (define-public tadbit
   (package
     (name "tadbit")
-    (version "0.2.0")
+    (version "1.0.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11212,21 +11237,13 @@ applications for tackling some common problems in a user-friendly way.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
+                "0hqrlymh2a2bimcfdvlssy1x5h1lp3h1c5a7jj11hmcqczzqn3ni"))))
     (build-system python-build-system)
     (arguments
-     `(;; Tests are included and must be run after installation, but
-       ;; they are incomplete and thus cannot be run.
-       #:tests? #f
-       #:python ,python-2
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-problems-with-setup.py
            (lambda* (#:key outputs #:allow-other-keys)
-             ;; setup.py opens these files for writing
-             (chmod "_pytadbit/_version.py" #o664)
-             (chmod "README.rst" #o664)
-
              ;; Don't attempt to install the bash completions to
              ;; the home directory.
              (rename-file "extras/.bash_completion"
@@ -11238,15 +11255,25 @@ applications for tackling some common problems in a user-friendly way.")
                                "/etc/bash_completion.d\""))
                (("extras/\\.bash_completion")
                 "extras/tadbit"))
+             #t))
+         (replace 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "python3" "test/test_all.py")
              #t)))))
+    (native-inputs
+     `(("glib" ,glib "bin")             ;for gtester
+       ("pkg-config" ,pkg-config)))
     (inputs
      ;; TODO: add Chimera for visualization
      `(("imp" ,imp)
        ("mcl" ,mcl)
-       ("python2-scipy" ,python2-scipy)
-       ("python2-numpy" ,python2-numpy)
-       ("python2-matplotlib" ,python2-matplotlib)
-       ("python2-pysam" ,python2-pysam)))
+       ("python-future" ,python-future)
+       ("python-h5py" ,python-h5py)
+       ("python-scipy" ,python-scipy)
+       ("python-numpy" ,python-numpy)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pysam" ,python-pysam)))
     (home-page "https://3dgenomes.github.io/TADbit/")
     (synopsis "Analyze, model, and explore 3C-based data")
     (description