Installation stops

[m.chaib....@rug.nl]

Hello, I am trying to install Anvi'o in my Linux Ubuntu using the recommended bash script.
However, it always stops for hours at:

python-scipy is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Reading package lists... Done
Building dependency tree      
Reading state information... Done
libhdf5-serial-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Requirement already satisfied (use --upgrade to upgrade): bottle in /usr/local/lib/python2.7/dist-packages
Cleaning up...
Requirement already satisfied (use --upgrade to upgrade): pysam in /usr/local/lib/python2.7/dist-packages
Cleaning up...
Downloading/unpacking hcluster
  Downloading hcluster-0.2.0.tar.gz (453kB): 453kB downloaded
  Running setup.py (path:/tmp/pip_build_root/hcluster/setup.py) egg_info for package hcluster

And then nothing happens. Do yo know how could I make the installation move forward?
Thanks!

Maryam

[Özcan Esen]

Hello Maryam,

I think i remember this problem, hcluster is wrongly packaged and needs user input when installing it in some situations, but it does not show it to you what it wants, so thats why it waits forever. You should manually install hcluster with "sudo pip install hcluster" or download the tarball at https://pypi.python.org/pypi/hcluster and install it with "sudo python setup.py install". One of this methods should ask you something like "select 1 or 2" (I can not remember exactly what it asks) then it will be installed successfully.

Best,
Özcan

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
---
You received this message because you are subscribed to the Google Groups "Anvi'o" group.
To unsubscribe from this group and stop receiving emails from it, send an email to anvio+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/anvio/7316782e-8165-426f-9e1d-1d738915d601%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[m.chaib....@rug.nl]

Dear Özcan,

Thank you for your suggestions!
Option number two worked for me. I downloaded the tarball at https://pypi.python.org/pypi/hcluster and installed it using sudo python setup.py install.

This message appeared in the terminal:

There are several valid include directories containing numpy/arrayobject.h
1: /usr/lib/python2.7/dist-packages
2: /usr/local/lib/python2.7/dist-packages
Selection [default=1]:

I selected 1.
Then, I went back and tried again with the recommended bash script. Finally I got the installation right. Thanks again!

Maryam