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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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can't use scenicplus command line and trouble in run_scenicplus #399

Closed Linshiqi-Git closed 5 months ago

Linshiqi-Git commented 6 months ago

Hi, I installed scenicplus according to the code below, but I cannot use the command line of scenicplus.

$ conda create --name scenicplus python=3.11 -y
$ conda activate scenicplus
$ git clone https://github.com/aertslab/scenicplus
$ cd scenicplus
$ pip install .

Version Python 3.8.18 scenicplus.version '1.0.1.dev6+ge5ba6fc.d20240321' ray.version '2.9.2'

Additionally, I have completed all the steps required to start SCENIC+ analysis, however, I encountered the error "UnboundLocalError: local variable 'tfs_to_genes' referenced before assignment" when running run_scenicplus. 

from scenicplus.wrappers.run_scenicplus import run_scenicplus
run_scenicplus(
    scplus_obj = scplus_obj,
    variable = ['predictedGroup'],
    species = 'hsapiens',
    assembly = 'hg19',
    tf_file = './outs/custom_cistarget/ref_db/utoronto_human_tfs_v_1.01.txt',
    save_path = os.path.join('./outs/run_scenicplus'),
    biomart_host = 'http://may2024.archive.ensembl.org/',
    upstream = [1000, 150000],
    downstream = [1000, 150000],
    calculate_TF_eGRN_correlation = True,
    calculate_DEGs_DARs = True,
    export_to_loom_file = True,
    export_to_UCSC_file = True,
    path_bedToBigBed = './outs/custom_cistarget/ref_db',
    n_cpu = 1,
    _temp_dir = os.path.join('./tmp/ray_spill'))

I learned from the issue(https://github.com/aertslab/scenicplus/issues/89) that it can be solved using snakemake, but my server cannot connect to network and I can't use the command line. Could you please help me with this problem?

Thank you very much in advance,

Kind regards