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authorRicardo Wurmus <rekado@elephly.net>2023-05-05 15:36:09 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-05-05 15:39:29 +0200
commit0b5088a2a3c7f78b79d3619a7be321d625514223 (patch)
tree0f3a6ff95270339154ab715fef5221c24b62dc93
parent5eac2bbb714cdf833b50e6515219e1cbfe7ad2df (diff)
gnu: Add python-genomepy.
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm53
1 files changed, 53 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4b2c0693d5..474b955bd0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5190,6 +5190,59 @@ HMMs).")
high-throughput sequencing (HTS) assays")
(license license:gpl3+)))
+(define-public python-genomepy
+ (package
+ (name "python-genomepy")
+ (version "0.15.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "genomepy" version))
+ (sha256
+ (base32
+ "0jmyvnsn6w0djjmxh4fjspy1346337jzihxb276v3s275r6zjmln"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; The tests require internet access.
+ #:tests? #false
+ #:phases
+ '(modify-phases %standard-phases
+ ;; Needed by tests
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs (list python-appdirs
+ python-biopython
+ python-click
+ python-colorama
+ python-diskcache
+ ;; We cannot use an older filelock, because the
+ ;; @lock annotation is used here.
+ python-filelock-3.5
+ python-loguru
+ python-mygene
+ python-mysql-connector-python
+ python-norns
+ python-numpy
+ python-pandas
+ python-pyfaidx
+ python-requests
+ python-tqdm))
+ (native-inputs (list python-hatchling python-pytest))
+ (home-page "https://vanheeringen-lab.github.io/genomepy/")
+ (synopsis "Genes and genomes at your fingertips")
+ (description "genomepy is designed to provide a simple and straightforward
+way to download and use genomic data. This includes
+
+@enumerate
+@item searching available data,
+@item showing the available metadata,
+@item automatically downloading, preprocessing and matching data, and
+@item generating optional aligner indexes.
+@end enumerate
+
+All with sensible, yet controllable defaults.")
+ (license license:expat)))
+
(define-public java-htsjdk
(package
(name "java-htsjdk")