diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 79 |
1 files changed, 53 insertions, 26 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b051389ae2..1a82815e92 100644 --- 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 |