phylophlan no longer available

[amojarro]

Hello,

following the "10 minute install" - hg clone https://bitbucket.org/nsegata/phylophlan does not work as Bitbucket no longer supports Mercurial repositories.

I tried installing phylophlan with conda install phylophlan, pip install phylophlan, and using the GitHub repository but I still receive the following error:

Activating conda environment: /home/mojarro/MAGpy/.snakemake/conda/3ff88c87 mkdir: cannot create directory ‘./phylophlan/input/205367’: No such file or directory cp: target './phylophlan/input/205367' is not a directory /bin/bash: line 3: cd: ./phylophlan: No such file or directory /bin/bash: line 4: ./phylophlan.py: No such file or directory mv: cannot stat './output/205367/*.nwk': No such file or directory mv: cannot stat './output/205367/*.xml': No such file or directory /bin/bash: line 8: ./phylophlan.py: No such file or directory mv: cannot stat './output/205367/*.nwk': No such file or directory mv: cannot stat './output/205367/*.txt': No such file or directory Waiting at most 5 seconds for missing files. MissingOutputException in line 109 of /home/mojarro/MAGpy/MAGpy: Job completed successfully, but some output files are missing. Missing files after 5 seconds: tree/MAGpy/MAGpy.tree.nwk This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. File "/home/mojarro/Documents/MiniConda3/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 544, in handle_job_success File "/home/mojarro/Documents/MiniConda3/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 231, in handle_job_success Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/mojarro/MAGpy/.snakemake/log/2020-08-20T114738.178383.snakemake.log

Any suggestions?

[mw55309]

If you have PhyloPhlAn installed using conda, then you need to edit the config file to tell MAGpy where it's installed

See https://github.com/WatsonLab/MAGpy/blob/master/config.json

You will see by default the PhyloPhlAn directory is "./phylophlan" which is where all your errors are coming from

I basically need to update MAGpy to use the conda version, but finding time is the issue....

[amojarro]

So after some trial and error I figured out that the environment called by MAGpy for PhyloPhlAn is Python 2.7

Activating conda environment: /home/mojarro/Documents/MAGs/MAGpy/.snakemake/conda/71dbf22f

I had initially downloaded PhyloPhlAn 3.0 but then found the PhyloPhlAn 1.0 release and got it to work.