Diginorm Installation

[rkizen]

Hello,

Does anyone have experience with installing Diginorm in a linux server without root access? The installation guide assumes you are using Amazon EC2 and have root access:

http://ged.msu.edu/angus/diginorm-2012/tutorial.html

I tried installing on a virtual box ubuntu machine where I had root access and I still ran into issues. When I ran ~/khmer/scripts/normalize-by-median.py it said that the khmer module could not be found. But running make for khmer didn't help. Seems like other people may have had issues installing as well:

https://biomickwatson.wordpress.com/2013/03/14/

While trying to install on the server where I do not have root access I altered the paths but I suspect there may be some hard set paths in the installation files somehwere. Any help is much appreciated! Thank you.

[lorendarith]

While trying to install on the server where I do not have root access I altered the paths but I suspect there may be some hard set paths in the installation files somehwere. Any help is much appreciated! Thank you.

Yeah, the tutorial does not take some things into account...

Anyway, since you do not have root permissions I do believe you have the PYTHONPATH variable with the location of the folder where you install your python libraries already exported. If you've already installed screed successfully, all you need to do is append the khmer path to the PYTHONPATH variable

So you should have something like:
export PYTHONPATH=/whatever/path/to/the/library/folder/

Add:
export PYTHONPATH=/whatever/path/to/the/library/folder/:/path/to/khmer/python/

Note that "khmer/python" is in the folder which you cloned from github after the make test command. After you changed the bashrc or bash_profile, start a new terminal and try running the "/khmer/scripts/normalize-by-median.py" script and it should work.

Hope this helps...

[rkizen]

Thank you lorendarith. It seems to be working now. I wonder why the installation guide assumes you will have root access.

[crusoe]

I know that this is an old thread but as the lead developer on khmer I wanted to clear a few things up.

Firstly, thanks for using our software!

We've revamped the installation process considerably in the last year. I agree, assuming root access is not a good idea.

https://khmer.readthedocs.org/en/v1.1/install.html

I am very happy to help with any other khmer related issues. Alas I haven't found a way to receive an alert whenever someone mentions khmer on seqanswers. In the mean time please feel free to alert us via GitHub about any issues:

https://github.com/ged-lab/khmer/issues

Or you can email us: [email protected]

Cheers,

[amitbik]

Error in using normalize-by-median.py

Hi, crusoe

An error is coming while using normalize-by-median.py.

python normalize-by-median.py -h

Traceback (most recent call last):
File "normalize-by-median.py", line 19, in <module>
import screed
ImportError: No module named screed

If i am running any command also i am getting the same error. Is there any problem with python?

Please help me..

Thanks in advance..

[crusoe]

Hello amitbik,

Looks like we resolved your problem over email. The next release of khmer included expanded installation instructions. They can be previewed at http://khmer.readthedocs.org/en/late...r/install.html

Cheers,

--
Michael R. Crusoe

[amitbik]

Hi Crusoe

Thanks a ton.. It is working fine now.... I will be waiting for next release of khmer.

Cheers,
--
Amit