write_default_configs.sh missing

[biobakery]

write_default_configs.sh missing

[fasnicar]

Dear Nick,

thanks for reporting this. I think you've installed an old PhyloPhlAn package that had the above issue, which has been fixed in the latest package available in Bioconda.
So, can you re-try after updating the package to the latest one?

Many thanks for your comments and

1. This should be fixed in the new package
2. I started re-writing PhyloPhlAn a few years ago and simply didn't like logging at that time, so end up defining two printing functions, nothing more than this
3. I don't see any problem in adding this parameter, and I think it is quite easy to add

Many thanks,
Francesco

[nick-youngblut]

I am using the most up-to-date bioconda build. The folder does not exists error may be due to re-installing phylophlan via python setup.py install into the conda env in order to incorporate my code edits (a --max_proteins param for phylophlan_setup_database). Maybe adding the default config files to package_data in setup.py would make this easier?

I searched through the repo, but I can't find write_default_configs.sh. I'm guessing that the CLI help doc was referring to phylophlan_write_default_configs.sh. I ran this, but the example 01 phylophlan job returns the error:

[e] configuration file "isolates_config.cfg" not found
Available configuration files in "configs":
    configs/supermatrix_aa.cfg
    configs/supermatrix_nt.cfg
    configs/supertree_aa.cfg
    configs/supertree_nt.cfg

It appears that phylophlan_write_default_configs.sh doesn't generate the "isolates_config.cfg" file specified in Example 01. I can't find any other reference to "isolates_config.cfg" in the repo.

[fasnicar]

I am using the most up-to-date bioconda build. The folder does not exists error may be due to re-installing phylophlan via python setup.py install into the conda env in order to incorporate my code edits (a --max_proteins param for phylophlan_setup_database). Maybe adding the default config files to package_data in setup.py would make this easier?

Strange, if you look at the setup.py in the repo (https://github.com/biobakery/phylophlan/blob/master/setup.py) we removed the generation of the default configs from there and put the phylophlan_write_default_configs.sh as a script. accordingly, we updated the Installation section of the user manual (https://github.com/biobakery/phylophlan/wiki#conda-package-easy), explicating now that the user should run the phylophlan_write_default_configs.sh script.
We can't provide default configs using he package_data in the setup.py as the configs are generated based on what executables are found in the system at run time.
Maybe I am missing something here.

I searched through the repo, but I can't find write_default_configs.sh. I'm guessing that the CLI help doc was referring to phylophlan_write_default_configs.sh. I ran this, but the example 01 phylophlan job returns the error:

Thanks, I corrected the typo in the code.

It appears that phylophlan_write_default_configs.sh doesn't generate the "isolates_config.cfg" file specified in Example 01. I can't find any other reference to "isolates_config.cfg" in the repo.

It doesn't as the phylophlan_write_default_configs.sh is a utility the easily generates 4 general configuration files for the user. Though, how to generate the config files used in the first example using the phylophlan_write_config_file command are reported in the tutorial (end of Step 3 and 4, respectively) https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3.0:-Example-01:-S.-aureus.

I hope these are helping.