[ASK]Could not install ChIP-AP in windows10 WSL

[Ci-TJ]

Hi! Thanks for developing ChIP-AP. I tried to install ChIP-AP in win10 WSL, but failed. Following is the detail. How should I deal with it?

(base) xy@DESKTOP-ILQK2F5:~/tools/chipap/chipap_installation$ ./chipap_installer.py
Anaconda directory is /home/xy/anaconda3
Do you want to install ChIP-AP in a specific environment? (Y/N) Y
Please type in the name of your ChIP-AP environment: chipap
ChIP-AP will be installed in chipap environment. Press ENTER to continue
Traceback (most recent call last):
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 16, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 70, in main_subshell
    p = generate_parser()
        ^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 65, in generate_parser
    p = ArgumentParser(
        ^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 152, in __init__
    self._subcommands = context.plugin_manager.get_hook_results("subcommands")
                        ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/base/context.py", line 502, in plugin_manager
    from ..plugins.manager import get_plugin_manager
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/plugins/__init__.py", line 3, in <module>
    from .hookspec import hookimpl  # noqa: F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/plugins/hookspec.py", line 9, in <module>
    from .types import CondaSolver, CondaSubcommand, CondaVirtualPackage
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/plugins/types.py", line 7, in <module>
    from ..core.solve import Solver
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 41, in <module>
    from .index import _supplement_index_with_system, get_reduced_index
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/index.py", line 22, in <module>
    from .package_cache_data import PackageCacheData
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/package_cache_data.py", line 421
    # At this point, we can assume the package tarbal
                                                     ^
IndentationError: expected an indented block after 'except' statement on line 420

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/xy/anaconda3/bin/conda", line 13, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 129, in main
    return conda_exception_handler(main, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 376, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 19, in __call__
    return self.handle_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 75, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 88, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 159, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/main_info.py", line 15, in <module>
    from ..core.index import _supplement_index_with_system
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/index.py", line 22, in <module>
    from .package_cache_data import PackageCacheData
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/package_cache_data.py", line 421
    # At this point, we can assume the package tarbal
                                                     ^
IndentationError: expected an indented block after 'except' statement on line 420
find: ‘/home/xy/anaconda3/envs/chipap’: No such file or directory
+ perl '/home/xy/anaconda3/envs/chipap/share/homer*/.//configureHomer.pl' -install hg38
Can't open perl script "/home/xy/anaconda3/envs/chipap/share/homer*/.//configureHomer.pl": No such file or directory

(base) xy@DESKTOP-ILQK2F5:~/tools/chipap/chipap_installation$ ./chipap_installer.py
Anaconda directory is /home/xy/anaconda3
Do you want to install ChIP-AP in a specific environment? (Y/N) N
ChIP-AP will be installed in base environment. Press ENTER to continue
Traceback (most recent call last):
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 16, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 70, in main_subshell
    p = generate_parser()
        ^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 65, in generate_parser
    p = ArgumentParser(
        ^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 152, in __init__
    self._subcommands = context.plugin_manager.get_hook_results("subcommands")
                        ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/base/context.py", line 502, in plugin_manager
    from ..plugins.manager import get_plugin_manager
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/plugins/__init__.py", line 3, in <module>
    from .hookspec import hookimpl  # noqa: F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/plugins/hookspec.py", line 9, in <module>
    from .types import CondaSolver, CondaSubcommand, CondaVirtualPackage
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/plugins/types.py", line 7, in <module>
    from ..core.solve import Solver
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/solve.py", line 41, in <module>
    from .index import _supplement_index_with_system, get_reduced_index
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/index.py", line 22, in <module>
    from .package_cache_data import PackageCacheData
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/package_cache_data.py", line 421
    # At this point, we can assume the package tarbal
                                                     ^
IndentationError: expected an indented block after 'except' statement on line 420

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/xy/anaconda3/bin/conda", line 13, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 129, in main
    return conda_exception_handler(main, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 376, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 19, in __call__
    return self.handle_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 75, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 88, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 159, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/cli/main_info.py", line 15, in <module>
    from ..core.index import _supplement_index_with_system
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/index.py", line 22, in <module>
    from .package_cache_data import PackageCacheData
  File "/home/xy/anaconda3/lib/python3.11/site-packages/conda/core/package_cache_data.py", line 421
    # At this point, we can assume the package tarbal
                                                     ^
IndentationError: expected an indented block after 'except' statement on line 420
+ perl '/home/xy/anaconda3/share/homer*/.//configureHomer.pl' -install hg38
^[[ACan't open perl script "/home/xy/anaconda3/share/homer*/.//configureHomer.pl": No such file or directory

Best, Seager

[mbassalbioinformatics]

Hi Seager Alright so we've never seen this error before so it may take a while for us (together) to get to the root of this. From what I understand from the error, it is having issues finding the configureHomer.pl script.

So ill need you to try 2 things for me please and then reply with what you see. 1 - delete the conda env and try running the installer again. Take note of any potential error message it brings up in trying to install homer

conda remove --name chipap --all

2 - if it fails with the same error message, please go through the folder structure and see where the homer configureHomer.pl script is located. It is supposed to be in

/home/xy/anaconda3/share/homer*/.//configureHomer.pl

(which is the last line in the error message above). If its not there then you need to find where its located/where it got installed and report that new path here please.

Will wait for your replies

[Ci-TJ]

@mbassalbioinformatics Hi! Sorry for late reply. I don't know why. I degraded annaconda, then the installation is successful. Maybe the software of the former annoconda env conflict to the chip-ap.