diff options
| author | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2020-11-24 02:15:16 -0500 |
|---|---|---|
| committer | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2020-11-24 02:20:32 -0500 |
| commit | 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64 (patch) | |
| tree | 29887391cd82ee695098da8c719ccf129e3f8fee /gnu | |
| parent | e7e73f750fa276c66995f3b9967dd2639be19cf8 (diff) | |
gnu: tadbit: Update to 1.0.1.
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1.
[arguments]: Remove #:tests? and #:python arguments.
[phases]{fix-problems-with-setup.py}: Remove no longer needed steps.
{check}: Override phase.
[native-inputs]: Add glib and pkg-config.
[inputs]: Add python-future and python-h5py.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 33 |
1 files changed, 18 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bd5a32a9b7..b3b4d1e1c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -66,6 +66,7 @@ #: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) @@ -11227,7 +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 @@ -11236,21 +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" @@ -11262,15 +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 |