diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 55 |
1 files changed, 28 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9765f1a178..fdb42562e8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1839,19 +1839,25 @@ the phenotype as it models the data.") (license license:asl2.0))) (define-public pbtranscript-tofu - (let ((commit "c7bbd5472")) + (let ((commit "8f5467fe6")) (package (name "pbtranscript-tofu") - (version (string-append "0.4.1." commit)) + (version (string-append "2.2.3." commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/cDNA_primer.git") (commit commit))) - (file-name (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx")))) + "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled Cython sources + (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -1861,34 +1867,29 @@ the phenotype as it models the data.") #:configure-flags '("--single-version-externally-managed" "--record=pbtranscript-tofu.txt") #:phases - (alist-cons-after - 'unpack 'enter-directory-and-clean-up - (lambda _ - (chdir "pbtranscript-tofu/pbtranscript/") - ;; Delete clutter - (delete-file-recursively "dist/") - (delete-file-recursively "build/") - (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/") - (delete-file-recursively "pbtools.pbtranscript.egg-info") - (delete-file "Cython-0.20.1.tar.gz") - (delete-file "setuptools_cython-0.2.1-py2.7.egg") - (delete-file "setuptools_cython-0.2.1.tar.gz") - (delete-file "setup.cfg") - (for-each delete-file - (find-files "." "\\.so$")) - ;; files should be writable for install phase - (for-each (lambda (f) (chmod f #o755)) - (find-files "." "\\.py$"))) - %standard-phases))) + (modify-phases %standard-phases + (add-after 'unpack 'enter-directory + (lambda _ + (chdir "pbtranscript-tofu/pbtranscript/") + #t)) + ;; With setuptools version 18.0 and later this setup.py hack causes + ;; a build error, so we disable it. + (add-after 'enter-directory 'patch-setuppy + (lambda _ + (substitute* "setup.py" + (("if 'setuptools.extension' in sys.modules:") + "if False:")) + #t))))) (inputs - `(("python-cython" ,python2-cython) - ("python-numpy" ,python2-numpy) + `(("python-numpy" ,python2-numpy) ("python-bx-python" ,python2-bx-python) ("python-networkx" ,python2-networkx) ("python-scipy" ,python2-scipy) - ("python-pbcore" ,python2-pbcore))) + ("python-pbcore" ,python2-pbcore) + ("python-h5py" ,python2-h5py))) (native-inputs - `(("python-nose" ,python2-nose) + `(("python-cython" ,python2-cython) + ("python-nose" ,python2-nose) ("python-setuptools" ,python2-setuptools))) (home-page "https://github.com/PacificBiosciences/cDNA_primer") (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") |