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-rw-r--r--gnu/packages/bioinformatics.scm55
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")