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[PATCH] Fix and update pbtranscript-tofu.
From: |
Ricardo Wurmus |
Subject: |
[PATCH] Fix and update pbtranscript-tofu. |
Date: |
Wed, 28 Oct 2015 14:47:30 +0100 |
>From eec9e45e681b5f2c85db8a5a60a0d55e132e62a1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Wed, 28 Oct 2015 14:39:13 +0100
Subject: [PATCH] gnu: pbtranscript-tofu: Update to 2.2.3.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
[source]: Remove bundled Cython sources in a snippet. Drop ".tar.gz"
extension from file-name field.
[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.
---
gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++--------------------
1 file changed, 28 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5aab152..44ad1ed 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1938,19 +1938,25 @@ 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))
(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
@@ -1960,34 +1966,29 @@ 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")
--
2.1.0
- [PATCH] Fix and update pbtranscript-tofu.,
Ricardo Wurmus <=