adamdingliang
commented
4 years ago Hi guozihuaa,
Thanks for your suggestions. cwltool is compatible with Microsoft Windows when Docker is installed: https://github.com/common-workflow-language/cwltool/blob/master/windowsdoc.md. Unfortunately, we don't have docker images built for SJARACNe yet.
As we haven't tested on a Windows platform, the easiest way I can think of for now is to find an unix-based platform to run. An alternative way, which is manual, is to use the Makefile in SJARACNe/SJARACNe directory and build the binary and run each step in SJARACNe/SJARACNe/bin manually.
j-andrews7
I have installed ANACONDA, python3.6 environemnt and all required packages, but when I run this script, I get error infromations.
(python3.6) D:\Users\guozi\Anaconda3\pkgs\SJARACNe-master>sjaracne local -e .\test_data\inputs\BRCA100.exp -g .\test_data\inputs\tf.txt -n 2 -o .\test_data\outputs\finaldata\outdata.txt INFO:root:test_data\outputs\finaldata\outdata.txt\sjaracne_workflow.yml INFO:root:exp_file: class: File path: D:\Users\guozi\Anaconda3\pkgs\SJARACNe-master\test_data\inputs\BRCA100.exp probe_file: class: File path: D:\Users\guozi\Anaconda3\pkgs\SJARACNe-master\test_data\inputs\tf.txt p_value_consensus: 1e-05 p_value_bootstrap: 1e-07 depth: 40 aracne_config_dir: class: Directory path: D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\sjaracne-0.2.0-py3.6.egg\SJARACNe/config bootstrap_num: 2 final_out_dir_name: outdata.txt INFO:root:cwltool --parallel --outdir .\test_data\outputs\finaldata\outdata.txt D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\sjaracne-0.2.0-py3.6.egg\SJARACNe/cwl/sjaracne_workflow.cwl test_data\outputs\finaldata\outdata.txt\sjaracne_workflow.yml [30mINFO[0m D:\Users\guozi\Anaconda3\envs\python3.6\Scripts\cwltool 1.0.20190618201008 Traceback (most recent call last): File "D:\Users\guozi\Anaconda3\envs\python3.6\Scripts\cwltool-script.py", line 11, in <module> load_entry_point('cwltool==1.0.20190618201008', 'console_scripts', 'cwltool')() File "D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\cwltool-1.0.20190618201008-py3.6.egg\cwltool\main.py", line 915, in run sys.exit(main(*args, **kwargs)) File "D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\cwltool-1.0.20190618201008-py3.6.egg\cwltool\main.py", line 640, in main fetcher_constructor=loadingContext.fetcher_constructor) File "D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\cwltool-1.0.20190618201008-py3.6.egg\cwltool\load_tool.py", line 89, in resolve_tool_uri raise ValidationException("Not found: '%s'" % argsworkflow) schema_salad.exceptions.ValidationException: Not found: 'D:UsersguoziAnaconda3envspython3.6libsite-packagessjaracne-0.2.0-py3.6.eggSJARACNe/cwl/sjaracne_workflow.cwl' Traceback (most recent call last): File "D:\Users\guozi\Anaconda3\envs\python3.6\Scripts\sjaracne-script.py", line 11, in <module> load_entry_point('SJARACNe==0.2.0', 'console_scripts', 'sjaracne')() File "D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\sjaracne-0.2.0-py3.6.egg\SJARACNe\sjaracne.py", line 99, in main run_shell_command_call(cmd) File "D:\Users\guozi\Anaconda3\envs\python3.6\lib\site-packages\sjaracne-0.2.0-py3.6.egg\SJARACNe\sjaracne.py", line 110, in run_shell_command_call subprocess.check_call(cmd_to_exec) File "D:\Users\guozi\Anaconda3\envs\python3.6\lib\subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cwltool', '--parallel', '--outdir', '.test_dataoutputsfinaldataoutdata.txt', 'D:UsersguoziAnaconda3envspython3.6libsite-packagessjaracne-0.2.0-py3.6.eggSJARACNe/cwl/sjaracne_workflow.cwl', 'test_dataoutputsfinaldataoutdata.txtsjaracne_workflow.yml']' returned non-zero exit status 1.it seems that, the cwltool package can not detect the right directory. I run this in Anacoda prompt. Could you fix this? This program is really important for my research.