diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 0 insertions, 57 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 610575230f..9674992955 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5618,63 +5618,6 @@ which automatically learns an optimal warping function (or transformation) for the phenotype as it models the data.") (license license:asl2.0))) -(define-public pbtranscript-tofu - (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) - (package - (name "pbtranscript-tofu") - (version (string-append "2.2.3." (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/PacificBiosciences/cDNA_primer") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "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 - ;; FIXME: Tests fail with "No such file or directory: - ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" - #:tests? #f - #: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-numpy" ,python2-numpy) - ("python-bx-python" ,python2-bx-python) - ("python-networkx" ,python2-networkx) - ("python-scipy" ,python2-scipy) - ("python-pbcore" ,python2-pbcore) - ("python-h5py" ,python2-h5py))) - (native-inputs - `(("python-cython" ,python2-cython) - ("python-nose" ,python2-nose))) - (home-page "https://github.com/PacificBiosciences/cDNA_primer") - (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") - (description - "pbtranscript-tofu contains scripts to analyze transcriptome data -generated using the PacBio Iso-Seq protocol.") - (license license:bsd-3)))) - (define-public prank (package (name "prank") |