diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 153 |
1 files changed, 149 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 13bd51860d..22b70a136f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -111,6 +111,7 @@ #:use-module (gnu packages jupyter) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages logging) #:use-module (gnu packages lsof) #:use-module (gnu packages machine-learning) @@ -830,13 +831,13 @@ servers supporting the protocol.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.8.2") + (version "0.9.0") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151")))) + "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj")))) (build-system python-build-system) (arguments `(#:modules ((srfi srfi-26) @@ -896,11 +897,16 @@ servers supporting the protocol.") (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description - "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, + "This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or \"genome algebra\". pybedtools extends BEDTools by offering feature-level manipulations from with Python.") - (license license:gpl2+))) + ;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in + ;; version 0.9.0 and the LICENSE.txt is consistant with the source code. + ;; + ;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are + ;; licensed lgpl2.1+ + (license (list license:expat license:lgpl2.1+)))) (define-public python-biom-format (package @@ -13375,6 +13381,145 @@ information... The package can also be used to extract data from @code{.loom} files.") (license license:expat)))) +(define-public python-ctxcore + (package + (name "python-ctxcore") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/ctxcore") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16nlj7z8pirgjad7vlgm7226b3hpw4a7n967vyfg26dsf5n8k70d")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'pretend-version + ;; The version string is usually derived via setuptools-scm, but + ;; it doesn't work without the .git directory. + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) + (propagated-inputs + (list python-cytoolz + python-numba + python-frozendict + python-numpy + python-pandas + python-pyyaml + python-pyarrow-0.16 + python-tqdm)) + (native-inputs + (list python-pytest + python-setuptools-scm)) + (home-page "https://github.com/aertslab/ctxcore") + (synopsis "Core functions for pycisTarget and the SCENIC tool suite") + (description + "ctxcore is part of the SCENIC suite of tools. It provides core functions for +pycisTarget and SCENIC.") + (license license:gpl3+))) + +(define-public python-arboreto + (package + (name "python-arboreto") + (version "0.1.6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/arboreto") + (commit "2f475dca08f47a60acc2beb8dd897e77b7495ca4"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0l0im8ay7l2d24f7vaha454vsaha9s36bfqhbijg3b8ir8apsd7l")))) + (build-system python-build-system) + ;; Lots of tests fail because python-distributed fails to start the + ;; "Nanny" process. + (arguments '(#:tests? #false)) + (propagated-inputs + (list python-bokeh + python-dask + python-distributed + python-numpy + python-pandas + python-scikit-learn + python-scipy + python-tornado-6)) + (home-page "https://github.com/aertslab/arboreto") + (synopsis "Gene regulatory network inference using tree-based ensemble regressors") + (description + "This package implements scalable gene regulatory network inference using +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 +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+))) + (define-public vbz-compression (package (name "vbz-compression") |