diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 93 |
1 files changed, 85 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c872c9c45a..92a299634f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2218,7 +2218,7 @@ well as many of the command line options.") (define-public bwa-meth (package (name "bwa-meth") - (version "0.2.2") + (version "0.2.3") (source (origin (method git-fetch) (uri (git-reference @@ -2227,7 +2227,7 @@ well as many of the command line options.") (file-name (git-file-name name version)) (sha256 (base32 - "17j31i7zws5j7mhsq9x3qgkxly6mlmrgwhfq0qbflgxrmx04yaiz")))) + "0c695lkrr0996zwkibl7324wg2vxmn6522sz30xv4a9gaf0lnbh3")))) (build-system python-build-system) (arguments `(#:phases @@ -2238,8 +2238,7 @@ well as many of the command line options.") (("bwa (mem|index)" _ command) (string-append (which "bwa") " " command)) ;; There's an ill-advised check for "samtools" on PATH. - (("^checkX.*") "")) - #t))))) + (("^checkX.*") ""))))))) (inputs (list bwa)) (native-inputs @@ -10895,6 +10894,9 @@ once. This package provides tools to perform Drop-seq analyses.") (add-before 'bootstrap 'autoreconf (lambda _ (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) (add-before 'check 'set-timezone ;; The readr package is picky about timezones. (lambda* (#:key inputs #:allow-other-keys) @@ -10969,7 +10971,10 @@ expression report comparing samples in an easily configurable manner.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ - (invoke "autoreconf" "-vif")))))) + (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (inputs (list grep coreutils @@ -11055,6 +11060,9 @@ in an easily configurable manner.") (add-before 'bootstrap 'autoreconf (lambda _ (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) (add-before 'check 'set-timezone ;; The readr package is picky about timezones. (lambda* (#:key inputs #:allow-other-keys) @@ -11123,7 +11131,10 @@ methylation and segmentation.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ - (invoke "autoreconf" "-vif")))))) + (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (native-inputs (list automake autoconf)) (inputs @@ -11197,7 +11208,10 @@ based methods.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ - (invoke "autoreconf" "-vif")))))) + (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (native-inputs (list automake autoconf)) (inputs @@ -12013,7 +12027,7 @@ implementation differs in these ways: python-igraph python-joblib python-legacy-api-wrap - python-louvain-0.6 + python-louvain-0.7 python-matplotlib python-natsort python-networkx @@ -15568,6 +15582,69 @@ aligner.") ;; bwa itself is licenced under GNU General Public License v3.0. (license license:mpl2.0))) +(define-public scvelo + (package + (name "scvelo") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scvelo" version)) + (sha256 + (base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (replace 'check + (lambda* (#:key outputs tests? #:allow-other-keys) + (when tests? + ;; The discovered test file names must match the names of the + ;; compiled files, so we cannot run the tests from + ;; /tmp/guix-build-*. + (with-directory-excursion + (string-append (assoc-ref outputs "out") + "/lib/python3.9/site-packages/scvelo/core/tests/") + (invoke "pytest" "-v")))))))) + (propagated-inputs + (list python-anndata + python-hnswlib + python-isort + python-igraph + python-loompy + python-louvain + python-matplotlib + python-numba + python-numpy + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-umap-learn + pybind11)) + (native-inputs + (list python-black + python-flake8 + python-hypothesis + python-pre-commit + python-pytest + python-setuptools-scm + python-wheel)) + (home-page "https://scvelo.org") + (synopsis "RNA velocity generalized through dynamical modeling") + (description "ScVelo is a scalable toolkit for RNA velocity analysis in +single cells. RNA velocity enables the recovery of directed dynamic +information by leveraging splicing kinetics. scVelo generalizes the concept of +RNA velocity by relaxing previously made assumptions with a stochastic and a +dynamical model that solves the full transcriptional dynamics. It thereby +adapts RNA velocity to widely varying specifications such as non-stationary +populations.") + (license license:bsd-3))) + (define-public scregseg (package (name "scregseg") |