# Installation problem

**URL:** <https://forum.biobakery.org/t/installation-problem/671>\
**Category:** PanPhlAn\
**Created:** [July 5, 2020, 8:57pm UTC](https://forum.biobakery.org/t/installation-problem/671 "2020-07-05T20:57:40Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Boyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/boyan/32/394_2.png) [@Boyan](https://forum.biobakery.org/u/Boyan)\
**Post date:** [July 5, 2020, 8:57pm UTC](https://forum.biobakery.org/t/installation-problem/671/1 "2020-07-05T20:57:40Z")

</div>

Hi,

I would like to analyze metagenomic data using PanPhlan. I download panphlan3 from [https://github.com/SegataLab/panphlan](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](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

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 6, 2020, 10:00am UTC](https://forum.biobakery.org/t/installation-problem/671/2 "2020-07-06T10:00:59Z")

</div>

PanPhlAn 3 is available in the 3.0 branch ([https://github.com/SegataLab/panphlan/tree/3.0](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`

---

<div class="post-metadata">

**Author:** ![Boyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/boyan/32/394_2.png) [@Boyan](https://forum.biobakery.org/u/Boyan)\
**Post date:** [July 7, 2020, 2:00am UTC](https://forum.biobakery.org/t/installation-problem/671/3 "2020-07-07T02:00:53Z")

</div>

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](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!!!

---

<div class="post-metadata">

**Author:** ![kescobo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kescobo/32/47_2.png) [@kescobo](https://forum.biobakery.org/u/kescobo)\
**Post date:** [September 9, 2020, 8:40pm UTC](https://forum.biobakery.org/t/installation-problem/671/5 "2020-09-09T20:40:34Z")

</div>

> [@Boyan](#):
>
> Is there any way I can bypass this problem?

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.