(address . guix-patches@gnu.org)(name . Navid Afkhami)(address . navid.afkhami@mdc-berlin.de)
0209ff8f7b80433fe8ab131a7de32a5ea049bbf3.1731519632.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-pybio): New variable.
Change-Id: I8f5c9cb6c7bb03cbc95386e67d46b1bdd78e01f2
---
gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
Toggle diff (66 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 599d22c51e..ddcb56d0c9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3223,6 +3223,57 @@ (define-public python-pybedtools
;; licensed lgpl2.1+
(license (list license:expat license:lgpl2.1+))))
+(define-public python-pybio
+ (let ((commit "c91fddc483da535d5097364405d76ad9b1bde07f")
+ (revision "1"))
+ (package
+ (name "python-pybio")
+ (version (git-version "0.3.12" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/grexor/pybio")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0s3n1bqp25zf5pzfsj0x1kqr6i2a6iffpb8hkjwhyvjqrxf5d9rk"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #f ;There are no automated tests
+ #:phases #~(modify-phases %standard-phases
+ (add-before 'check 'set-home
+ ;; The sanity check requires a HOME directory
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ (add-after 'unpack 'adjust-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("bs4")
+ "beautifulsoup4"))))
+ (add-after 'unpack 'build-reproducibly
+ (lambda _
+ (setenv "GUIX_BUILD" "yes")
+ (substitute* "pybio/__init__.py"
+ (("^pybio.core.genomes.init\\(\\)" m)
+ (string-append m
+ " if not os.getenv('GUIX_BUILD') else None"))))))))
+ (propagated-inputs (list python-beautifulsoup4 python-numpy
+ python-psutil python-pysam python-requests))
+ (native-inputs (list python-pytest))
+ (home-page "https://github.com/grexor/pybio")
+ (synopsis "Basic genomics toolset")
+ (description
+ "This tool provides a Python framework to streamline genomics operations.
+It offers a direct interface to Ensembl genome assemblies and annotations, while
+also accommodating custom genomes via FASTA/GTF inputs. The primary objective
+of pybio is to simplify genome management. It achieves this by providing
+automatic download of Ensembl genome assemblies and annotation, provides
+Python genomic feature search and sequence retrieval from the managed
+genomes, STAR indexing and mapping and more.")
+ (license license:gpl3+))))
+
(define-public python-ega-download-client
(package
(name "python-ega-download-client")
base-commit: 07cd046c209f192032b425d2ee44f6025bff63a1
--
2.43.0