Shouldn't you remove the requirements for fasta-db?

[miko8422]

It is a really hard job to deploy this thing to my local server, I mean...
So I have done all the pre-required installation, but still have this problem after I try to run
python bin/create_est_nextflow_params.py family --families PF07476 --output-dir $results_dir --efi-config /data/efi/efi.config --efi-db /data/efi/efi_202408.sqlite --nextflow-config conf/est/docker.config
Literally the same command you guys put in doc/source/guides/database.rst
It just does not work, it keeps asking me the parameter of fasta-db, you guys' demo command didn't even have this parameter...
Here is the folder structure of the dataset I downloaded:
blastdb diamonddb efi_db.sqlite

Sorry been a little anger on this, I know it is hard to maintain a big opensource project.

Can someone help me out?

[rbdavid]

Hi, the python script run in that command no longer accepts a default value for the fasta_db variable. It is likely our documentation for running the parameter file creation scripts is out of date. I've created a new issue to track documentation updates (#247). This issue (#245) will be used to track the specific python scripts' documentation inaccuracies.

Documentation updates for the EFI tools' CLI commands are currently on the back burner because we are actively developing the new web interface, enabling users to avoid the command line calls for EFI's complex set of tools. In the meantime, I suggest you run the testing suite suite and use the testing module scripts as the guides for how to run further command line calls of the tools.

[miko8422]

Hi, the python script run in that command no longer accepts a default value for the fasta_db variable. It is likely our documentation for running the parameter file creation scripts is out of date. I've created a new issue to track documentation updates (#247). This issue (#245) will be used to track the specific python scripts' documentation inaccuracies.

Documentation updates for the EFI tools' CLI commands are currently on the back burner because we are actively developing the new web interface, enabling users to avoid the command line calls for EFI's complex set of tools. In the meantime, I suggest you run the testing suite suite and use the testing module scripts as the guides for how to run further command line calls of the tools.

Yea, thanks, and hope we can get the new interface soon. I have fixed the problem, and get things settle in my server. I solved it with quote the downloaded fasta database's blastdb/combined.fasta. Thanks for the resources.

[miko8422]

Hi, the python script run in that command no longer accepts a default value for the fasta_db variable. It is likely our documentation for running the parameter file creation scripts is out of date. I've created a new issue to track documentation updates (#247). This issue (#245) will be used to track the specific python scripts' documentation inaccuracies.
Documentation updates for the EFI tools' CLI commands are currently on the back burner because we are actively developing the new web interface, enabling users to avoid the command line calls for EFI's complex set of tools. In the meantime, I suggest you run the testing suite suite and use the testing module scripts as the guides for how to run further command line calls of the tools.

Yea, thanks, and hope we can get the new interface soon. I have fixed the problem, and get things settle in my server. I solved it with quote the downloaded fasta database's blastdb/combined.fasta. Thanks for the resources.

Also tracking the issue (#245), I may update more information when issue was solved, thanks for you guys' hard work again. XD.