diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 243 |
1 files changed, 127 insertions, 116 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a414a58382..3e7b99ee61 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1070,11 +1070,11 @@ similar.") (license license:gpl2+)))) (define-public r-stringendo - (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01") + (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a") (revision "1")) (package (name "r-stringendo") - (version (git-version "0.3.4" revision commit)) + (version (git-version "0.6.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -1083,10 +1083,10 @@ similar.") (file-name (git-file-name name version)) (sha256 (base32 - "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v")))) + "15ij4zf2j9c8m9n4bqhmxkchjh2bhddwjfxngfpwv7c5wjqyi6ir")))) (properties `((upstream-name . "Stringendo"))) (build-system r-build-system) - (propagated-inputs (list r-devtools r-usethis)) + (propagated-inputs (list r-clipr)) (home-page "https://github.com/vertesy/Stringendo") (synopsis "Stringendo is a string parsing library") (description @@ -1095,11 +1095,11 @@ plotnames, filenames and paths.") (license license:gpl3)))) (define-public r-readwriter - (let ((commit "12d32cb6533ef4b9eab4d707d1502525c2034aee") + (let ((commit "91373c44641014a1ce8e1c3e928747608aae8f54") (revision "1")) (package (name "r-readwriter") - (version (git-version "0.3.2" revision commit)) + (version (git-version "1.5.3" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -1108,11 +1108,11 @@ plotnames, filenames and paths.") (file-name (git-file-name name version)) (sha256 (base32 - "1hy47g8d7zppr2i9zlkwl2yb0ii8x710hqk07h089ldx9171qxab")))) + "156kvmplrip0w1zhs9yl5r0ayjipa0blhy614l65hbsjn1lwbskr")))) (properties `((upstream-name . "ReadWriter"))) (build-system r-build-system) (propagated-inputs - (list r-gdata r-gtools r-openxlsx r-readr r-stringendo)) + (list r-gtools r-openxlsx r-readr r-stringendo)) (home-page "https://github.com/vertesy/ReadWriter") (synopsis "Functions to read and write files conveniently") (description @@ -10245,55 +10245,54 @@ auROC analysis.") (license license:gpl3)))) (define-public r-sccustomize - (let ((commit "8414d1f5fb32277855b0619191a568932b7baeb0") + (let ((commit "397374590dae2ccc0c560897dcd1ce4382c18798") (revision "1")) (package (name "r-sccustomize") - (version (git-version "0.7.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/samuel-marsh/scCustomize") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1wcgfq7lx83a2kf8pjbw524gdvxf351n08cwd5wzmmy57kf4knbj")))) + (version (git-version "2.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samuel-marsh/scCustomize") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11bafm0mlck27fqd8brz80pxb8dc5q0aqbp8zv0s9sx97njp7wsl")))) (properties `((upstream-name . "scCustomize"))) (build-system r-build-system) - (propagated-inputs - (list r-circlize - r-colorway - r-cowplot - r-data-table - r-dittoseq - r-dplyr - r-forcats - r-ggbeeswarm - r-ggplot2 - r-ggprism - r-ggpubr - r-ggrastr - r-ggrepel - r-glue - r-janitor - r-magrittr - r-matrix - r-paletteer - r-patchwork - r-pbapply - r-purrr - r-remotes - r-scales - r-scattermore - r-seurat - r-seuratobject - r-stringi - r-stringr - r-tibble - r-tidyr - r-tidyselect - r-viridis)) + (propagated-inputs (list r-circlize + r-colorway + r-cowplot + r-data-table + r-dittoseq + r-dplyr + r-forcats + r-ggbeeswarm + r-ggplot2 + r-ggprism + r-ggpubr + r-ggrastr + r-ggrepel + r-glue + r-janitor + r-magrittr + r-matrix + r-paletteer + r-patchwork + r-pbapply + r-purrr + r-remotes + r-scales + r-scattermore + r-seurat + r-seuratobject + r-stringi + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/samuel-marsh/scCustomize") (synopsis "Custom visualization and analyses of single-cell sequencing") @@ -15349,7 +15348,9 @@ activity prediction from transcriptomics data, and its R implementation (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - (list r-complexheatmap + (list r-basilisk + r-basilisk-utils + r-complexheatmap r-dplyr r-ggplot2 r-magrittr @@ -17988,7 +17989,7 @@ updated much more frequently.") (define-public python-ctxcore (package (name "python-ctxcore") - (version "0.1.1") + (version "0.2.0") (source (origin (method git-fetch) @@ -17998,8 +17999,8 @@ updated much more frequently.") (file-name (git-file-name name version)) (sha256 (base32 - "16nlj7z8pirgjad7vlgm7226b3hpw4a7n967vyfg26dsf5n8k70d")))) - (build-system python-build-system) + "0nv4lc46cnzpg5gcdxrsv7b4srmkq55zl3rcadw5pn3yyz5fzd2k")))) + (build-system pyproject-build-system) (arguments (list #:phases @@ -18011,12 +18012,12 @@ updated much more frequently.") (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) (propagated-inputs (list python-cytoolz - python-numba python-frozendict + python-numba python-numpy python-pandas + python-pyarrow python-pyyaml - python-pyarrow-0.16 python-tqdm)) (native-inputs (list python-pytest @@ -18064,67 +18065,77 @@ tree-based ensemble regressors.") (license license:bsd-3))) (define-public pyscenic - (package - (name "pyscenic") - (version "0.11.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/aertslab/pySCENIC") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0pbmmr1zdb1vbbs6wx357s59d13pna6x03wq8blj6ckjws8bbq73")))) - (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 _ - (invoke "pytest" "-v")))))) - (propagated-inputs - (list python-ctxcore - python-cytoolz - python-multiprocessing-on-dill - python-llvmlite - python-numba - python-attrs - python-frozendict - python-numpy - python-pandas - python-cloudpickle - python-dask - python-distributed - python-arboreto - python-boltons - python-setuptools - python-pyyaml - python-tqdm - python-interlap - python-umap-learn - python-loompy - python-networkx - python-scipy - python-fsspec - python-requests - python-aiohttp - python-scikit-learn)) - (native-inputs - (list python-pytest)) - (home-page "https://scenic.aertslab.org/") - (synopsis "Single-Cell regulatory network inference and clustering") - (description - "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell + ;; Latest commit from the update-pyarrow branch + (let ((commit "5f170fdf474548c37ab381d1849c662820d658ee") + (revision "1")) + (package + (name "pyscenic") + (version (git-version "0.11.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/pySCENIC") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03qkvy400rjndg2ds6bhcaprir71mqr2v3yv9vd77lcnzxgw3s0z")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; The cli modules referenced here have been removed, so this + ;; breaks the sanity check. + (add-after 'unpack 'do-not-reference-deleted-modules + (lambda _ + (substitute* "setup.py" + (("'db2feather = .*',") "") + (("'invertdb = .*',") "") + (("'gmt2regions = pyscenic.cli.gmt2regions:main'") "")))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs + (list python-ctxcore + python-cytoolz + python-multiprocessing-on-dill + python-llvmlite + python-numba + python-attrs + python-frozendict + python-numpy + python-pandas + python-cloudpickle + python-dask + python-pyarrow ;XXX for dask + python-distributed + python-arboreto + python-boltons + python-setuptools + python-pyyaml + python-tqdm + python-interlap + python-umap-learn + python-loompy + python-networkx + python-scipy + python-fsspec + python-requests + python-aiohttp + python-scikit-learn)) + (native-inputs + (list python-pytest)) + (home-page "https://scenic.aertslab.org/") + (synopsis "Single-Cell regulatory network inference and clustering") + (description + "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public python-ikarus (package |