gnu: emacs-clj-refactor: Update to 3.11.3. - guix

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author	Nicolas Goaziou <mail@nicolasgoaziou.fr>	2024-01-21 23:41:34 +0100
committer	Nicolas Goaziou <mail@nicolasgoaziou.fr>	2024-01-22 00:20:53 +0100
commit	303765a0ec7d2f2a68957ca29df1e802b6fc076c (patch)
tree	a8e9d2e1084e732a59c753d2085a29f0623ca97f /gnu/installer/services.scm
parent	15bdc7215ba0c9125a661b9c59a60b02861d7307 (diff)
download	guix-303765a0ec7d2f2a68957ca29df1e802b6fc076c.tar.gz guix-303765a0ec7d2f2a68957ca29df1e802b6fc076c.zip

gnu: emacs-clj-refactor: Update to 3.11.3.

* gnu/packages/emacs-xyz.scm (emacs-clj-refactor): Update to 3.11.3. Change-Id: Ifd6131fa4c1360785c2a8e061353f269fcb1c23d

Diffstat (limited to 'gnu/installer/services.scm')

0 files changed, 0 insertions, 0 deletions

40bc121a7..1837ad0bc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm

@@ -2149,7 +2149,7 @@ databases.")

(define-public clipper

(package

(name "clipper")

- (version "1.2.1")

+ (version "2.0")

(source (origin

(method git-fetch)

(uri (git-reference

@@ -2158,40 +2158,34 @@ databases.")

(file-name (git-file-name name version))

(sha256

(base32

- "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))

- (modules '((guix build utils)))

- (snippet

- '(begin

- ;; remove unnecessary setup dependency

- (substitute* "setup.py"

- (("setup_requires = .*") ""))

- #t))))

+ "1bcag4lb5bkzsj2vg7lrq24aw6yfgq275ifrbhd82l7kqgbbjbkv"))))

(build-system python-build-system)

(arguments

- `(#:python ,python-2 ; only Python 2 is supported

- #:phases

+ `(#:phases

(modify-phases %standard-phases

- ;; This is fixed in upstream commit

- ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb.

- (add-after 'unpack 'fix-typo

- (lambda _

- (substitute* "clipper/src/readsToWiggle.pyx"

- (("^sc.*") ""))

- #t)))))

+ (add-before 'reset-gzip-timestamps 'make-files-writable

+ (lambda* (#:key outputs #:allow-other-keys)

+ ;; Make sure .gz files are writable so that the

+ ;; 'reset-gzip-timestamps' phase can do its work.

+ (let ((out (assoc-ref outputs "out")))

+ (for-each make-file-writable

+ (find-files out "\\.gz$"))

+ #t))))))

(inputs

- `(("htseq" ,python2-htseq)

- ("python-pybedtools" ,python2-pybedtools)

- ("python-cython" ,python2-cython)

- ("python-scikit-learn" ,python2-scikit-learn)

- ("python-matplotlib" ,python2-matplotlib)

- ("python-pandas" ,python2-pandas)

- ("python-pysam" ,python2-pysam)

- ("python-numpy" ,python2-numpy)

- ("python-scipy" ,python2-scipy)))

+ `(("htseq" ,htseq)

+ ("python-pybedtools" ,python-pybedtools)

+ ("python-cython" ,python-cython)

+ ("python-scikit-learn" ,python-scikit-learn)

+ ("python-matplotlib" ,python-matplotlib)

+ ("python-pandas" ,python-pandas)

+ ("python-pysam" ,python-pysam)

+ ("python-numpy" ,python-numpy)

+ ("python-scipy" ,python-scipy)))

(native-inputs

- `(("python-mock" ,python2-mock) ; for tests

- ("python-nose" ,python2-nose) ; for tests

- ("python-pytz" ,python2-pytz))) ; for tests

+ `(("python-setuptools-git" ,python-setuptools-git)

+ ("python-mock" ,python-mock) ; for tests

+ ("python-nose" ,python-nose) ; for tests

+ ("python-pytz" ,python-pytz))) ; for tests

(home-page "https://github.com/YeoLab/clipper")

(synopsis "CLIP peak enrichment recognition")

(description


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