Comments (3)
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
- This should be fixed in the new package
- 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
- I don't see any problem in adding this parameter, and I think it is quite easy to add
Many thanks,
Francesco
from phylophlan.
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.
from phylophlan.
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.
from phylophlan.
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