annejong / bagel4 Goto Github PK

Hello devs! Thanks as ever for the great resource. I'm currently trying to get it working, but am getting a HTML file with no content in the gene AOI pages, when using the sample data as suggested by the installation process.

I've clearly gone wrong somewhere in setup, but don't know how/where/what module to troubleshoot this under...

Any suggestions would be much appreciated.
thanks,
C.H.

Hi, I'm not good at programming, so I used the BAGEL4 web-based tool.
I have a whole genome sequence, sequenced with Pacbio and Illuminaseq sequencing and then assembled.
So, I enter FastA file of my sequence, but it didn't work!

But I have no idea about this problem.
How can I solve it?

Thanks!

Hello, I've tried to migrate from web-based to stand-alone version of BAGEL4 using Linux, following the steps on "README.md". Unfortunately, the instruction indicating "To download all dependencies, click here" directs you to a "404 error webpage".
After downloading, unpacking, indexing and configuring the necessary folders and files, the message I have when I'm at bagel4 folder and try to run "./bagel4_wrapper.pl" is
"Can't locate anne_files.pm in @inc (you may need to install the anne_files module) (@inc contains: /home/iagolbm/anaconda3/lib/site_perl/5.34.0/x86_64-linux-thread-multi /home/iagolbm/anaconda3/lib/site_perl/5.34.0 /home/iagolbm/anaconda3/lib/5.34.0/x86_64-linux-thread-multi /home/iagolbm/anaconda3/lib/5.34.0 .) at ./bagel4_wrapper.pl line 23.
BEGIN failed--compilation aborted at ./bagel4_wrapper.pl line 23."

Is it due to any common mistake during installation/configuration? Does it have another recommended way to install the program?
Thank you for the attention.

Hi there,
Could you please update the manual of the local Linux version? The existing one does not work, and I even cannot find the configuration file "bagel4.conf" in the github package. Thanks!