From f700223c3bb7e80104c7c011edcd09479145bb26 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 16 Jun 2022 15:19:44 +0200
Subject: gnu: Add pyscenic.

* gnu/packages/bioinformatics.scm (pyscenic): New variable.
---
 gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e6b14069ec..75973b0dd8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13457,6 +13457,69 @@ pycisTarget and SCENIC.")
 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")
-- 
cgit 1.4.1