nafkhamdc wrote 1 years ago
(address . guix-patches@gnu.org)(name . nafkhamdc)(address . navid.afkhami@mdc-berlin.de)
bb1b0092bc31e21d2745955d2e3d83cb1ca5003c.1707942466.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-ega-download-client): New variable.
Change-Id: I3233774975989f912281ab2e6ec6ad3362cae18b
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
Toggle diff (52 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bcfe3c2656..863bf1ff26 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2525,6 +2525,43 @@ (define-public python-pybedtools
;; licensed lgpl2.1+
(license (list license:expat license:lgpl2.1+))))
+(define-public python-ega-download-client
+ (package
+ (name "python-ega-download-client")
+ (version "5.1.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/EGA-archive/ega-download-client")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0k9rfq2yyvfxs5sq9lsm8krp9ddx4s18hv85ikf3b37zv24kpwjk"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags '(list "-k"
+ ;; These tests fail because they require internet access.
+ (string-append "not test_download.py"
+ " and not test_htsget.py"
+ " and not test_commands.py"))
+ #:phases '(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("==")
+ ">=")))))))
+ (propagated-inputs (list python-htsget python-psutil python-requests
+ python-tqdm python-urllib3))
+ (native-inputs (list python-coverage python-pytest python-pyfakefs
+ python-responses))
+ (home-page "https://github.com/EGA-archive/ega-download-client")
+ (synopsis "EGA download client: pyEGA3")
+ (description
+ "PyEGA3 is a tool for viewing and downloading files from authorized EGA datasets.")
+ (license license:asl2.0)))
+
(define-public python-scdamandtools
(package
(name "python-scdamandtools")
base-commit: 2ba2875dbda4b080fcad4e6d672bb4104d59dd0c
--
2.34.1