cadnano2.5 not running on Windows 10 after installation

[blackwellbert]

After installing according to instructions and using the command "cadnano" in dos shell from cadnano2.5 directory, I get the following output:

C:\Users\pparr\OneDrive\Documents\GitHub\cadnano2.5>cadnano Traceback (most recent call last): File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\Scripts\cadnano-script.py", line 33, in sys.exit(load_entry_point('cadnano==2.5.2.1', 'console_scripts', 'cadnano')()) File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\bin\main.py", line 36, in main app = initAppWithGui(argv, do_exec=False) File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano__init.py", line 65, in initAppWithGui shared_app.finishInit() File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\cadnanoqt.py", line 103, in finishInit from cadnano.document import Document File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\document.py", line 38, in from cadnano.fileio.decode import decodeFile File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\fileio\decode.py", line 6, in import cadnano.fileio.v2decode as v2decode File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\fileio\v2decode.py", line 18, in from cadnano.part.nucleicacidpart import DEFAULT_RADIUS File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\part\nucleicacidpart.py", line 40, in from cadnano.strandset import SplitCommand, StrandSet File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\strandset\init__.py", line 1, in from .strandset import * File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\strandset\strandset.py", line 22, in from .removestrandcmd import RemoveStrandCommand File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\strandset\removestrandcmd.py", line 4, in from cadnano.views.pathview import pathstyles File "C:\Users\pparr\AppData\Local\Programs\Python\Python310\lib\site-packages\cadnano\views\pathview\pathstyles.py", line 178, in XOVER_LABEL_FONT = QFont(THE_FONT, THE_FONT_SIZE/2, QFont.Light) TypeError: arguments did not match any overloaded call: QFont(): too many arguments QFont(str, pointSize: int = -1, weight: int = -1, italic: bool = False): argument 2 has unexpected type 'float' QFont(QFont, QPaintDevice): argument 1 has unexpected type 'str' QFont(QFont): argument 1 has unexpected type 'str' QFont(Any): too many arguments

However, when I run the command "cadnano2' from the same directory, cadnano2.4 runs. So why does the 2.4 version run but not the 2.5 version as shown by the errors above? Or am I missing something?

Thanks in advance for your help!

[sdouglas]

In general, we probably need to start working on porting cadnano2.5 over to PyQt6.

In the meantime, I think this particular bug can be fixed by casting the QFont parameter as an int — I saw similar behavior with cadnano2.

I’ll try to take a look within the next week or so.

[blackwellbert]

Thanks for your email! Is it possible to use “autobreak”? If so, how do I activate it?

On Sun, Jul 24, 2022 at 5:04 PM Shawn Douglas @.***> wrote:

In general, we probably need to start working on porting cadnano2.5 over to PyQt6.

In the meantime, I think this particular bug can be fixed by casting the QFont parameter as an int — I saw similar behavior with cadnano2.

I’ll try to take a look within the next week or so.

— Reply to this email directly, view it on GitHub https://github.com/cadnano/cadnano2.5/issues/194#issuecomment-1193402521, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKOKSAQIR5VSYRX52QKVVTTVVW4WHANCNFSM54M2K4RQ . You are receiving this because you authored the thread.Message ID: @.***>

[sdouglas]

The old algorithm did not select very good break positions, so we removed it to encourage users to break staples manually. Our lab has been building a new algorithm that gives even better results, based on applying a global optimization to minimize scaffold looping entropy. This is not yet published, but I hope to launch it as a web-based tool in the coming months, where you will be able to upload cadnano files and apply the algorithm to perform a highly optimized autobreak.

In the meantime, I recommend breaking manually using the the "Rule 3" heuristic from this paper: https://www.nature.com/articles/ncomms2095

[blackwellbert]

Thanks for the info! I will check it out!

On Fri, Aug 5, 2022 at 3:22 PM Shawn Douglas @.***> wrote:

The old algorithm did not select very good break positions, so we removed it to encourage users to break staples manually. Our lab has been building a new algorithm that gives even better results, based on applying a global optimization to minimize scaffold looping entropy. This is not yet published, but I hope to launch it as a web-based tool in the coming months, where you will be able to upload cadnano files and apply the algorithm to perform a highly optimized autobreak.

In the meantime, I recommend breaking manually using the the "Rule 3" heuristic from this paper: https://www.nature.com/articles/ncomms2095 https://urldefense.com/v3/__https://www.nature.com/articles/ncomms2095__;!!LQC6Cpwp!uqCLewq1BCo3sVhAqVMNigJIV4ribrsWgGlFNmNRj55qNEoGGtN7IyN5N-mUXmkY3F307wCPmC8L2p6qAa7p9uJY64mVwmdD5P1ay9IS_A$

— Reply to this email directly, view it on GitHub https://github.com/cadnano/cadnano2.5/issues/194#issuecomment-1206832889, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKOKSAQ5VVCSA6HY4IGISKLVXVZWPANCNFSM54M2K4RQ . You are receiving this because you authored the thread.Message ID: @.***>

[RodenLuo]

Any news about the AutoBreak? Either in Cadnano or the web-based tool? Thanks.