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gnu: pbtranscript-tofu: Update to 2.2.3.

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* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
  [source]: Remove bundled Cython sources in a snippet.  Replace
  ".tar.gz" extension in file-name field with "-checkout".
  [arguments]: Replace "enter-directory-and-clean-up" phase with
  "enter-directory" phase, and add "patch-setuppy" phase.
  [inputs]: Add python2-h5py.  Move python2-cython ...
  [native-inputs]: ... to this field.
This commit is contained in:
Ricardo Wurmus 2015-10-28 14:39:13 +01:00
parent fb8d1be8e1
commit 9a067efdb2
1 changed files with 28 additions and 27 deletions
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55
gnu/packages/bioinformatics.scm
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@ -1839,19 +1839,25 @@ (define-public python2-warpedlmm
(license license:asl2.0))) (license license:asl2.0)))
(define-public pbtranscript-tofu (define-public pbtranscript-tofu
(let ((commit "c7bbd5472")) (let ((commit "8f5467fe6"))
(package (package
(name "pbtranscript-tofu") (name "pbtranscript-tofu")
(version (string-append "0.4.1." commit)) (version (string-append "2.2.3." commit))
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/PacificBiosciences/cDNA_primer.git") (url "https://github.com/PacificBiosciences/cDNA_primer.git")
(commit commit))) (commit commit)))
(file-name (string-append name "-" version ".tar.gz")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (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) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2 `(#:python ,python-2
@ -1861,34 +1867,29 @@ (define-public pbtranscript-tofu
#:configure-flags '("--single-version-externally-managed" #:configure-flags '("--single-version-externally-managed"
"--record=pbtranscript-tofu.txt") "--record=pbtranscript-tofu.txt")
#:phases #:phases
(alist-cons-after (modify-phases %standard-phases
'unpack 'enter-directory-and-clean-up (add-after 'unpack 'enter-directory
(lambda _ (lambda _
(chdir "pbtranscript-tofu/pbtranscript/") (chdir "pbtranscript-tofu/pbtranscript/")
;; Delete clutter #t))
(delete-file-recursively "dist/") ;; With setuptools version 18.0 and later this setup.py hack causes
(delete-file-recursively "build/") ;; a build error, so we disable it.
(delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/") (add-after 'enter-directory 'patch-setuppy
(delete-file-recursively "pbtools.pbtranscript.egg-info") (lambda _
(delete-file "Cython-0.20.1.tar.gz") (substitute* "setup.py"
(delete-file "setuptools_cython-0.2.1-py2.7.egg") (("if 'setuptools.extension' in sys.modules:")
(delete-file "setuptools_cython-0.2.1.tar.gz") "if False:"))
(delete-file "setup.cfg") #t)))))
(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)))
(inputs (inputs
`(("python-cython" ,python2-cython) `(("python-numpy" ,python2-numpy)
("python-numpy" ,python2-numpy)
("python-bx-python" ,python2-bx-python) ("python-bx-python" ,python2-bx-python)
("python-networkx" ,python2-networkx) ("python-networkx" ,python2-networkx)
("python-scipy" ,python2-scipy) ("python-scipy" ,python2-scipy)
("python-pbcore" ,python2-pbcore))) ("python-pbcore" ,python2-pbcore)
("python-h5py" ,python2-h5py)))
(native-inputs (native-inputs
`(("python-nose" ,python2-nose) `(("python-cython" ,python2-cython)
("python-nose" ,python2-nose)
("python-setuptools" ,python2-setuptools))) ("python-setuptools" ,python2-setuptools)))
(home-page "https://github.com/PacificBiosciences/cDNA_primer") (home-page "https://github.com/PacificBiosciences/cDNA_primer")
(synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")