diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 111 |
1 files changed, 88 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9ce28596c2..87e7c33b90 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3312,6 +3312,77 @@ off-target reads for a capture method that targets CpG-rich region.") multiple sequence alignments.") (license license:expat))) +(define-public python-mofax + ;; This is a recent commit from the "dev" branch, which is much more recent + ;; than the latest commit from the "master" branch. + (let ((commit "4d96f8f0a5d5251847353656f523684d66c3c47a") + (revision "0")) + (package + (name "python-mofax") + (version (git-version "0.4.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioFAM/mofax") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lwrw0qyvvnyiqz1l20dhcf7dxidb80cqgvk78czvdgba87yxzqx")) + (modules '((guix build utils))) + ;; Prevent the pyproject-build-system from guessing that flit + ;; should be used as a builder. + (snippet '(substitute* "pyproject.toml" + (("^#.*") ""))))) + (build-system pyproject-build-system) + (arguments + (list + ;; This test is failing due to a bug. The bug has been reported to the + ;; developers. See https://github.com/bioFAM/mofax/issues/12 for more + ;; info. + #:test-flags '(list "-k" "not test_get_methods"))) + (propagated-inputs (list python-h5py + python-matplotlib + python-pandas + python-poetry-core + python-scipy + python-seaborn)) + (native-inputs (list python-numpy python-pytest)) + (home-page "https://github.com/bioFAM/mofax") + (synopsis + "Motif activity finder for transcription factor motif analysis") + (description + "MoFax is a Python package for transcription factor motif analysis. +It provides convenience functions to load and visualize factor models trained +with MOFA+ in Python.") + (license license:expat)))) + +(define-public python-mudata + (package + (name "python-mudata") + (version "0.2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/scverse/mudata") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02h0k1q57589r0hdv8nwg1vk7g2ljvn5g66c47fy5gdilbm3gjws")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-anndata python-h5py python-pandas)) + (native-inputs + (list python-flit-core python-numpy python-pytest python-zarr)) + (home-page "https://github.com/scverse/mudata") + (synopsis "Python package for multi-omics data analysis") + (description + "Mudata is a Python package for multi-omics data analysis. +It is designed to provide functionality to load, process, and store multimodal +omics data.") + (license license:bsd-3))) + (define-public python-pyega3 (package (name "python-pyega3") @@ -10805,34 +10876,34 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") (define-public bioruby (package (name "bioruby") - (version "1.5.2") + (version "2.0.4") (source (origin (method url-fetch) (uri (rubygems-uri "bio" version)) (sha256 (base32 - "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) + "08aknxk2ingwscwfqpw5vnax6jpk1sxfaialravladb63hcl8dx9")))) (build-system ruby-build-system) (propagated-inputs (list ruby-libxml)) (native-inputs (list which)) ; required for test phase (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'patch-test-command - (lambda _ - (substitute* '("test/functional/bio/test_command.rb") - (("/bin/sh") (which "sh"))) - (substitute* '("test/functional/bio/test_command.rb") - (("/bin/ls") (which "ls"))) - (substitute* '("test/functional/bio/test_command.rb") - (("which") (which "which"))) - (substitute* '("test/functional/bio/test_command.rb", - "test/data/command/echoarg2.sh") - (("/bin/echo") (which "echo"))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'patch-test-command + (lambda _ + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/sh") (which "sh"))) + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/ls") (which "ls"))) + (substitute* '("test/functional/bio/test_command.rb") + (("which") (which "which"))) + (substitute* '("test/functional/bio/test_command.rb" + "test/data/command/echoarg2.sh") + (("/bin/echo") (which "echo")))))))) (synopsis "Ruby library, shell and utilities for bioinformatics") (description "BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has @@ -11661,13 +11732,7 @@ using high-throughput sc-RNAseq data.") (copy-file (string-append "bin/sambamba-" ,version) (string-append bin "/sambamba")))))))) (native-inputs - `(("ld-gold-wrapper" - ;; Importing (gnu packages commencement) would introduce a cycle. - ,(module-ref (resolve-interface - '(gnu packages commencement)) - 'ld-gold-wrapper)) - ("binutils-gold" ,binutils-gold) - ("python" ,python))) + (list python)) (inputs (list ldc lz4 zlib)) (home-page "https://github.com/biod/sambamba") |