installation on a cluster

[Thomieh73]

Hi, I am trying to install MicrobeCensus on the abel computing cluster here in Oslo, Norway. The cluster runs on linux 64 bit Centos 6

Since I lack sufficient permissions, I followed your alternative installation suggestion. I can load python2 (v2.7.10) since that has the biopython and numpy packages.

I have tested if I can import numpy and Bio.SeqIO on the python commandline. I can. These packages are installed in the folder:

/cluster/software/VERSIONS/python_packages-2.7_3/cluster/software/VERSIONS/python2-2.7.9/lib/python2.7/site-packages/

This folder is found in my $PYTHONPATH after loading python2.

Next I added microbecensus to the $PYTHONPATH and I added the scripts to the $PATH.

When I then call: run_microbe_census.py -h I get:

Could not import module 'numpy'

So I believe I have followed the correct way of setting this up, so I am surprised numpy is not found.

Do you have any idea on how I can solve this?

[Thomieh73]

Hi, I actually overcame the installation issue on our cluster

I Installed MicrobeCensus using pip on my area on the computing cluster using the command:

pip install --user MicrobeCensus

after that I add the line to my .bash_profile file to point to the file run_microbe_census.py

export PATH=$PATH:/usit/abel/u1/thhaverk/.local/bin

Now I can run the program easily.

So in the instructions add the --user flag for pip. That makes it easier if you are not a superuser. Thomas

ps. this tool runs well on my macbook.

[snayfach]

I've added that to the README on GitHub. Let me know if you have any other comments, questions, or suggestions. Thanks for using MicrobeCensus!