The bioBakery help forum

Installation problem

Hi,

I would like to analyze metagenomic data using PanPhlan. I download panphlan3 from https://github.com/SegataLab/panphlan. But I could not find any installation instructions on https://github.com/SegataLab/panphlan/wiki/Home_3_0#the-panphlan-steps.

I tried to install it by “python setup.py install” and got an error:
Traceback (most recent call last):
File “setup.py”, line 13, in
packages=setuptools.find_namespace_packages(),
AttributeError: module ‘setuptools’ has no attribute ‘find_namespace_packages’

I also tried to use the scripts directly under “/panphlan” and found that there was no file named “panphlan_download_pangenome.py” (but it was on the guidance on Github).

I would really appreciate it if you can help me solve these problems or give me some detailed guidance. Thank you so much!

Boyan

PanPhlAn 3 is available in the 3.0 branch (https://github.com/SegataLab/panphlan/tree/3.0), you need to switch branch using git checkout. The master branch currently hosts the 1.3 version.
For installing it, I recommend using pip install . instead python setup.py install

1 Like

Thank you so so much!!!
I have successfully installed PanPhlAn by “pip install PanPhlAn”. But I still have an error when downloading pangenome using panphlan_download_pangenome.py.
unable to download "https://www.dropbox.com/s/1gxpwk8ba0rmopp/panphlan_pangenomes_links.tsv?dl=1"
It is caused by SSL connection. It seems that downloading files from dropbox is not permitted on our public cluster.
Is there any way I can bypass this problem?
Thanks a lot!!!

You can download the file to your local system, and then transfer it to your cluster using scp or rsync. If it’s in the working directory where you call the script from (or maybe in the folder you designate with -o? For me, they’re the same thing) it seems to work.