summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm226
1 files changed, 132 insertions, 94 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8dffc86c00..c59c7fa5db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -29,6 +29,7 @@
;;; Copyright © 2024 Spencer King <spencer.king@geneoscopy.com>
;;; Copyright © 2025 nomike Postmann <nomike@nomike.com>
;;; Copyright © 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -78,6 +79,7 @@
#:use-module (gnu packages bison)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages certs)
#:use-module (gnu packages check)
#:use-module (gnu packages code)
#:use-module (gnu packages cmake)
@@ -2835,41 +2837,51 @@ specifying the usage of each program for each cell in the data.")
parsing of Variant Call Format (VCF) files.")
(license license:expat)))
-(define-public python-decoupler-py
+(define-public python-decoupler
(package
- (name "python-decoupler-py")
- ;; Upstream places release on a new branch, see
- ;; <https://github.com/saezlab/decoupler-py/issues/175>.
- (version "1.8.0")
+ (name "python-decoupler")
+ (version "2.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/saezlab/decoupler-py")
- (commit version)))
+ (url "https://github.com/scverse/decoupler")
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0c3yg7jjb1nxb6hsh9wn7wr8w0ba55gixdbf5fp443nhv1cwlajj"))))
+ "0b15n5sq940sn29jsgmdkkm4fcpzfq1n221scfwhjxb4ybdpsz4v"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
- '(list "-k"
- ;; These tests require internet access
- (string-append "not test_get_resource"
- " and not test_show_resources"
- " and not test_get_dorothea"
- " and not test_get_progeny"
- " and not test_get_ksn_omnipath"
- ;; This attempts to download things for Omnipath
- " and not test_get_collectri"))
+ '(list "-k" (string-join
+ ;; Tests requiring internet access to reach out
+ ;; <datasets.cellxgene.cziscience.com>, <ftp.ebi.ac.uk>,
+ ;; <omnipathdb.org>, <raw.githubusercontent.com>,
+ ;; <static.omnipathdb.org>, <www.ensembl.org>,
+ ;; <www.ncbi.nlm.nih.gov>, and <zenodo.org>.
+ (list "not test_collectri"
+ "test_covid5k"
+ "test_dorothea"
+ "test_download"
+ "test_download_anndata"
+ "test_ensmbl_to_symbol"
+ "test_erygast1k"
+ "test_hallmark"
+ "test_hsctgfb"
+ "test_knocktf"
+ "test_msvisium"
+ "test_pbmc3k"
+ "test_progeny"
+ "test_resource"
+ "test_show_resources"
+ "test_translate"
+ ;; XXX: Some precision mismatched.
+ "test_func_gsea"
+ "test_net_corr")
+ " and not "))
#:phases
'(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "pyproject.toml"
- ;; numba = "^0.60.0"; all tests passed.
- (("0.60.0") "0.61.0"))))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp")))
@@ -2878,27 +2890,35 @@ parsing of Variant Call Format (VCF) files.")
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (list python-adjusttext
python-anndata
- python-ipython
- python-matplotlib
- python-nbsphinx
+ python-dcor
+ python-docrep
+ python-igraph
+ python-ipywidgets
+ python-marsilea
python-numba
- python-numpy
- python-numpydoc
- python-omnipath
- python-scanpy
- python-scikit-learn
+ python-requests
python-scipy
- python-skranger
+ python-session-info2
python-tqdm
- python-typing-extensions))
- (native-inputs (list python-poetry-core python-pytest))
- (home-page "https://github.com/saezlab/decoupler-py")
+ python-xgboost))
+ (native-inputs
+ (list nss-certs-for-test
+ python-hatchling
+ python-gseapy
+ python-memory-profiler
+ python-pytest
+ python-scanpy))
+ (home-page "https://github.com/scverse/decoupler")
(synopsis
"Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
(description
"This package provides different statistical methods to extract
biological activities from omics data within a unified framework.")
- (license license:gpl3+)))
+ (license license:bsd-3)))
+
+;; See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>
+(define-public python-decoupler-py
+ (deprecated-package "python-decoupler-py" python-decoupler))
(define-public python-demuxem
(package
@@ -3119,16 +3139,16 @@ servers supporting the protocol.")
(define-public python-liana-py
(package
(name "python-liana-py")
- (version "1.4.0")
+ (version "1.6.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/saezlab/liana-py")
- (commit version)))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "1kwbhfmsjhfc6m4kcp4zc2xgzg1qf16ywfkdamn868anwwrvjxzb"))))
+ "1k6l371wd00m95l5pb2jsmzzxh5nc5v21fg2v0cslr9761q151r9"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -3159,27 +3179,30 @@ servers supporting the protocol.")
" and not test_bivar_product"
;; XXX unclear failure: large difference in data
;; frames.
- " and not test_aggregate_res")
+ " and not test_aggregate_res"
+ ;; XXX: ValueError: Only CSR and CSC matrices are
+ ;; supported.
+ " and not test_bivar_nondefault"
+ " and not test_masked_spearman"
+ " and not test_vectorized_spearman"
+ " and not test_basic_interpolation"
+ " and not test_different_methods"
+ " and not test_fill_value"
+ " and not test_use_raw_layer_parameters")
;; These need the optional squidpy, which we don't have yet.
- "--ignore=liana/tests/test_misty.py"
+ "--ignore=tests/test_misty.py"
;; These need the optional corneto.
- "--ignore=liana/tests/test_causalnet.py"
+ "--ignore=tests/test_causalnet.py"
;; Needs internet access.
- "--ignore=liana/tests/test_orthology.py")
+ "--ignore=tests/test_orthology.py")
#:phases
'(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- ;; Don't fail the sanity check when these optional inputs aren't
- ;; available.
- (substitute* "pyproject.toml"
- (("^pre-commit =.*") ""))))
;; Numba needs a writable directory to cache functions.
(add-before 'build 'set-numba-cache-dir
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (list python-anndata
python-cell2cell
- python-decoupler-py
+ python-decoupler
python-hypothesis
python-ipykernel
python-ipython
@@ -3199,10 +3222,8 @@ servers supporting the protocol.")
python-tqdm
tzdata))
(native-inputs
- (list python-black
- python-poetry-core
- python-pytest
- python-pytest-cov))
+ (list python-hatchling
+ python-pytest))
(home-page "https://github.com/saezlab/liana-py")
(synopsis "LIANA is a ligand-receptor analysis framework")
(description "This is a Ligand-Receptor inference framework. The
@@ -5012,7 +5033,7 @@ package provides command line tools using the Bio++ library.")
(define-public blast+
(package
(name "blast+")
- (version "2.14.0")
+ (version "2.17.0")
(source (origin
(method url-fetch)
(uri (string-append
@@ -5020,7 +5041,7 @@ package provides command line tools using the Bio++ library.")
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "003mn7m4y306k7visv3in3ikfgm8m41z0jq9lyvz10iv1hdpyixz"))
+ "0ix1bqgaywi3ggis4qvaipb0mk3llhgf52vmc97f744risl5f82h"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5636,7 +5657,7 @@ with MOFA+ in Python.")
(define-public python-mudata
(package
(name "python-mudata")
- (version "0.3.1")
+ (version "0.3.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -5645,7 +5666,7 @@ with MOFA+ in Python.")
(file-name (git-file-name name version))
(sha256
(base32
- "1m1qsqgk8snllavfj99qgm2j7cccviwg7k0k1kfbvqn0bkzc87sa"))))
+ "17s1w3746d35pcwr97ynhr7s5hfk76vsfcinwyqynx9k3xxi9br4"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -7071,16 +7092,16 @@ trees (phylogenies) and characters.")
(define-public python-py2bit
(package
(name "python-py2bit")
- (version "0.3.0")
+ (version "0.3.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "py2bit" version))
(sha256
(base32
- "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5"))))
+ "0w1p4l1jwg9kkifm0jsg33a212ps0jn61islmnng2afp77y5nkr6"))))
(build-system pyproject-build-system)
- (native-inputs (list python-setuptools python-wheel))
+ (native-inputs (list python-setuptools python-setuptools-scm python-wheel))
(home-page "https://github.com/dpryan79/py2bit")
(synopsis "Access 2bit files using lib2bit")
(description
@@ -8748,18 +8769,7 @@ HMMs).")
(sha256
(base32
"1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19"))))
- (build-system python-build-system)
- (arguments
- (list
- #:phases
- '(modify-phases %standard-phases
- ;; Avoid rebuilding the extension. Everything is built during the
- ;; 'install phase anyway.
- (delete 'build)
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-v")))))))
+ (build-system pyproject-build-system)
(propagated-inputs
(list python-matplotlib
python-numpy
@@ -8769,6 +8779,8 @@ HMMs).")
python-pandas
python-pytest
python-scipy
+ python-setuptools
+ python-wheel
swig))
(home-page "https://github.com/htseq")
(synopsis "Framework for analyzing high-throughput sequencing data")
@@ -17043,7 +17055,7 @@ The following file formats are supported:
(define-public salmon
(package
(name "salmon")
- (version "1.10.1")
+ (version "1.10.3")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -17052,7 +17064,7 @@ The following file formats are supported:
(file-name (git-file-name name version))
(sha256
(base32
- "0grpcajxf2bch4b74zb66pdssda8yc7jvxj5ckaw0xvw1605rpcj"))
+ "0vii7nlx0ddn62qniwx4abfj6ajwl3w6mizavpa0mkhpxnm06rqw"))
(modules '((guix build utils)))
(snippet
;; Delete bundled headers for eigen3.
@@ -17167,7 +17179,7 @@ The following file formats are supported:
(file-name (git-file-name "pufferfish" version))
(sha256
(base32
- "0fcv5rd2k4fabsg489sjfxgjisivhwk1w26gfc88rgpszdkcla36"))))))
+ "0h12h4wv7k3if1m6as7wvrbd7djm0zsg1vs0xn84bnrswwv5z2l3"))))))
(home-page "https://github.com/COMBINE-lab/salmon")
(synopsis "Quantification from RNA-seq reads using lightweight alignments")
(description "Salmon is a program to produce highly-accurate,
@@ -19738,7 +19750,7 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.10.4")
+ (version "1.11.2")
(source
(origin
(method git-fetch)
@@ -19748,12 +19760,14 @@ implementation differs in these ways:
(file-name (git-file-name name version))
(sha256
(base32
- "139d6fsdbhg1hqqq5yyl8hr3cqz2mj70i0i8r1mq6z6a8qmq1p4z"))))
+ "18ddb3jkyjan87f5kymyq951sa5955z41f10h6z954map8dy2136"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; 736 passed, 95 skipped, 20 xfailed, 148 warnings
#:test-flags
'(list "-m" "not gpu"
+ "--numprocesses" (number->string (parallel-job-count))
;; These tests require Internet access.
"--ignore-glob=tests/notebooks/*"
"--ignore=tests/test_clustering.py"
@@ -19771,9 +19785,10 @@ implementation differs in these ways:
"--ignore=tests/test_preprocessing.py"
"--ignore=tests/test_read_10x.py"
"--ignore=plotting/_tools/scatterplots.py"
- ;; The following tests requires 'scanorama', which isn't
- ;; packaged yet.
- "--ignore=tests/external/test_scanorama_integrate.py"
+ ;; Adding additional options does not help to resolve the
+ ;; faileur: TypeError: _FlakyPlugin._make_test_flaky() got an
+ ;; unexpected keyword argument 'reruns'.
+ "--ignore=tests/test_backed.py"
"-k"
;; Plot tests that fail.
(string-append "not test_clustermap"
@@ -19784,6 +19799,8 @@ implementation differs in these ways:
" and not test_paga_plots"
" and not test_violin"
" and not test_scatter_no_basis_per_obs"
+ " and not test_spatial_general"
+ " and not test_visium_empty_img_key"
;; These are doctests that fail because of missing
;; datasets.
@@ -19801,7 +19818,21 @@ implementation differs in these ways:
" and not test_pca_layer"
" and not test_pca_sparse"
" and not test_pca_reproducible"
- " and not test_clip"))
+ " and not test_clip"
+
+ ;; Missing test data.
+ " and not test_covariance_eigh_impls"
+ " and not test_embedding_colorbar_location"
+ " and not test_sparse_dask_input_errors"
+ " and not test_sparse_dask_input_errors"
+ " and not test_spatial_external_img"
+
+ ;; Somehow broken tests.
+ " and not test_sim_toggleswitch"
+ " and not scanpy.datasets._datasets.krumsiek11"
+ " and not scanpy.datasets._datasets.toggleswitch"
+ " and not scanpy.external.pp._scanorama_integrate.scanorama_integrate"
+ " and not scanpy.preprocessing._simple.filter_cells"))
#:phases
#~(modify-phases %standard-phases
;; XXX This should not be necessary, but I noticed while building
@@ -19825,9 +19856,12 @@ implementation differs in these ways:
(string-append (getcwd) ":"
#$(this-package-native-input "python-anndata:source") ":"
(getenv "GUIX_PYTHONPATH")))))
- ;; Numba needs a writable dir to cache functions.
- (add-before 'check 'set-numba-cache-dir
- (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Numba needs a writable dir to cache functions.
+ (setenv "NUMBA_CACHE_DIR" "/tmp")
+ ;; For Matplotlib.
+ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list python-anndata
python-dask
@@ -19843,27 +19877,30 @@ implementation differs in these ways:
python-packaging
python-pandas
python-patsy
+ python-pytoml
python-scikit-learn
python-scipy
- python-setuptools ; For pkg_resources.
python-seaborn
- python-session-info
+ python-session-info2
+ python-setuptools ; For pkg_resources.
python-sinfo
python-statsmodels
python-tables
- python-pytoml
python-tqdm
python-umap-learn))
(native-inputs
`(;; This package needs anndata.tests, which is not installed.
("python-anndata:source" ,(package-source python-anndata))
+ ("python-flaky" ,python-flaky)
("python-flit" ,python-flit)
- ("python-hatchling" ,python-hatchling)
("python-hatch-vcs" ,python-hatch-vcs)
+ ("python-hatchling" ,python-hatchling)
("python-leidenalg" ,python-leidenalg)
("python-pytest" ,python-pytest)
("python-pytest-mock" ,python-pytest-mock)
("python-pytest-nunit" ,python-pytest-nunit)
+ ("python-pytest-xdist" ,python-pytest-xdist)
+ ("python-scanorama" ,python-scanorama)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python")
@@ -22844,8 +22881,8 @@ pairs.")
(license license:expat)))
(define-public r-hdf5dataframe
- (let ((commit "1cdb905b1f6af3339938de3e1ca407908bc93e47")
- (revision "1"))
+ (let ((commit "1e30e6b82b5599d5d98fbcb8bf7312dd1711ca3c")
+ (revision "2"))
(package
(name "r-hdf5dataframe")
(version (git-version "0.0.0" revision commit))
@@ -22857,12 +22894,12 @@ pairs.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "1pk22h56x873gahj2nwnwxzyq5a27h363mxk1491irypvk78dpn9"))))
+ (base32 "0y6hp31gy17v87ll4rij6pwy6b7k7gnw8iwnvzsaa13ga73g69ak"))))
(properties `((upstream-name . "HDF5DataFrame")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics r-delayedarray r-hdf5array
r-rhdf5 r-s4vectors))
- (native-inputs (list r-knitr))
+ (native-inputs (list r-knitr r-testthat))
(home-page "https://github.com/BIMSBbioinfo/HDF5DataFrame")
(synopsis "Bioconductor-friendly bindings for Parquet")
(description
@@ -22997,6 +23034,7 @@ guix_python <- \"~a\";"
python-scipy
python-tifffile
python-zarr
+ which ;tests/testthat/test_conversion.R
zlib))
(propagated-inputs (list r-data-table
r-dplyr
@@ -23525,7 +23563,7 @@ compute communities on graphs weighted or unweighted.")
(define-public ivar
(package
(name "ivar")
- (version "1.4.2")
+ (version "1.4.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -23534,7 +23572,7 @@ compute communities on graphs weighted or unweighted.")
(file-name (git-file-name name version))
(sha256
(base32
- "0v3rsak84ilg4iaynwpmmkj507vham5rjk2pfsmylpaqylgc69yx"))))
+ "1bwygjv81m4yv5ycxb5gx22k6njgwrzzs7jrsadq6363klcv4irh"))))
(build-system gnu-build-system)
(arguments
(list
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-08 02:46:32 +0000