Afkhami, Navid wrote 1 years ago
(address . guix-patches@gnu.org)(name . Afkhami, Navid)(address . Navid.Afkhami@mdc-berlin.de)
777b97bec88e9beb56d7d57738eb9aba9956566e.1698760882.git.Navid.Afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-baltica): Update to 1.1.2.
[propagated-inputs]: Add r-yaml, r-rsamtools, r-biocmanager, r-here, r-genomicranges,
r-readr, r-tidyr, r-stringr, r-optparse, r-openxlsx, r-dplyr, and
r-upsetr.
Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676
---
gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++--------------
1 file changed, 43 insertions(+), 33 deletions(-)
Toggle diff (99 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a47e84bc33..66d1a21ffe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5130,47 +5130,57 @@ (define-public python-baltica
(package
(name "python-baltica")
(version "1.1.2")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/dieterich-lab/Baltica")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dieterich-lab/Baltica")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
(build-system pyproject-build-system)
(arguments
(list
- #:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- ;; The tests need to be run from elsewhere...
- (mkdir-p "/tmp/test")
- (copy-recursively ".tests" "/tmp/test")
- (with-directory-excursion "/tmp/test"
- (invoke "pytest" "-v" "--doctest-modules"))))))))
- (propagated-inputs
- (list gunicorn
- python-anndata
- python-click
- python-flask
- python-flask-wtf
- python-h5py
- python-numpy
- python-psutil
- python-pysam
- python-pyyaml
- python-scipy
- snakemake-7))
+ #:phases '(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; The tests need to be run from elsewhere...
+ (mkdir-p "/tmp/test")
+ (copy-recursively ".tests" "/tmp/test")
+ (with-directory-excursion "/tmp/test"
+ (invoke "pytest" "-v" "--doctest-modules"))))))))
+ (propagated-inputs (list gunicorn
+ python-anndata
+ python-click
+ python-flask
+ python-flask-wtf
+ python-h5py
+ python-numpy
+ python-psutil
+ python-pysam
+ python-pyyaml
+ python-scipy
+ r-yaml
+ r-rsamtools
+ r-biocmanager
+ r-here
+ r-genomicranges
+ r-readr
+ r-tidyr
+ r-stringr
+ r-optparse
+ r-openxlsx
+ r-dplyr
+ r-upsetr
+ snakemake-7))
(native-inputs (list python-cython python-pyfakefs python-pytest))
(home-page "https://github.com/dieterich-lab/Baltica")
(synopsis "Integrated splice junction usage analysis")
(description
"This framework facilitates the execution of @dfn{differential junction
-usage} (DJU) methods. Additionally, it enables the integration of results from
+usage} (DJU) methods. Additionally, it enables the integration of results from
multiple DJU methods.")
(license license:expat)))
base-commit: c0895371c5759c7d9edb330774e90f192cc4cf2c
--
2.34.1