SyntaxError: invalid syntax

[MathildaStigenberg]

Hi,

I need some help. I am working on a server and want to use SJARACNe. Unfortunately, I have encountered some problems. Firstly, I created an environment for SJARACNe following the tutorial by these commands: conda create -n sjaracne python=3.7.6 source activate sjaracne

Then, I got an error message when trying to install SJARACNe by using this command: pip install SJARACNe Error message: "ERROR: Ignored the following versions that require a different python version: 0.2.0 Requires-Python ==3.6.1 ERROR: Could not find a version that satisfies the requirement SJARACNe (from versions: none) ERROR: No matching distribution found for SJARACNe"

Instead, I tried to install SJARACNe by installing from source with these commands: git clone https://github.com/jyyulab/SJARACNe cd SJARACNe python setup.py build # build SJARACNe binary python setup.py install

I got a warning message: "warning: no files found matching '*.c' under directory 'msgpack' /disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!!"

Since I got no error messages when installing SJARACNe, I am trying to run SJARACNe with this command: sjaracne local -e /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/SJAR/project_2024-01-16/input.exp -g /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/SJAR/project_2024-01-16/sig.txt -o /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_sig -tmp /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_tf/tmp/

However, this caused an error message: "/disk1/mathilda/software/mambaforge/envs/sjaracne/bin/sjaracne:15: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import load_entry_point INFO:root:/disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_sig/sjaracne_workflow.yml INFO:root:exp_file: class: File path: /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/SJAR/project_2024-01-16/input.exp probe_file: class: File path: /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/SJAR/project_2024-01-16/sig.txt p_value_consensus: 1e-05 p_value_bootstrap: 1e-07 depth: 40 aracne_config_dir: class: Directory path: /disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/config bootstrap_num: 100 final_out_dir_name: output_sig INFO:root:cwltool --tmpdir-prefix /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_tf/tmp/ --parallel --outdir /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_sig /disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl /disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_sig/sjaracne_workflow.yml /disk1/mathilda/software/mambaforge/envs/sjaracne/bin/cwltool:15: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import load_entry_point Traceback (most recent call last): File "/disk1/mathilda/software/mambaforge/envs/sjaracne/bin/cwltool", line 33, in sys.exit(load_entry_point('cwltool==3.1.20240112164112', 'console_scripts', 'cwltool')()) File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/pkg_resources/init.py", line 536, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/pkg_resources/init.py", line 2928, in load_entry_point return ep.load() File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/pkg_resources/init.py", line 2516, in load return self.resolve() File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/pkg_resources/init.py", line 2522, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/cwltool-3.1.20240112164112-py3.7.egg/cwltool/main.py", line 39, in from schema_salad.exceptions import ValidationException File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/schema_salad-8.5.20240102191335-py3.7.egg/schema_salad/exceptions.py", line 4, in from .sourceline import SourceLine, reflow_all, strip_duplicated_lineno File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/schema_salad-8.5.20240102191335-py3.7.egg/schema_salad/sourceline.py", line 88 if (r := lineno_re.match(line)) is not None: ^ SyntaxError: invalid syntax Traceback (most recent call last): File "/disk1/mathilda/software/mambaforge/envs/sjaracne/bin/sjaracne", line 33, in sys.exit(load_entry_point('SJARACNe==0.2.1', 'console_scripts', 'sjaracne')()) File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/sjaracne.py", line 102, in main run_shell_command_call(cmd) File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/sjaracne.py", line 113, in run_shell_command_call subprocess.check_call(cmd_to_exec) File "/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cwltool', '--tmpdir-prefix', '/disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_tf/tmp/', '--parallel', '--outdir', '/disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_sig', '/disk1/mathilda/software/mambaforge/envs/sjaracne/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl', '/disk1/mathilda/hidden_drivers/test/test/project_2024-01-16/output_sig/sjaracne_workflow.yml']' returned non-zero exit status 1."

I seem to have the correct versions of packages, but it doesn't work unfortunately and I am not sure how to proceed. Thanks in advance for your help.