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| author | Ricardo Wurmus <rekado@elephly.net> | 2023-05-05 15:36:09 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-05-05 15:39:29 +0200 |
| commit | 0b5088a2a3c7f78b79d3619a7be321d625514223 (patch) | |
| tree | 0f3a6ff95270339154ab715fef5221c24b62dc93 /gnu/packages | |
| parent | 5eac2bbb714cdf833b50e6515219e1cbfe7ad2df (diff) | |
| download | guix-0b5088a2a3c7f78b79d3619a7be321d625514223.tar.gz guix-0b5088a2a3c7f78b79d3619a7be321d625514223.zip | |
gnu: Add python-genomepy.
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
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") |