[khmer] Khmer error

C. Titus Brown ctb at msu.edu
Wed Jul 2 11:35:04 PDT 2014


On Wed, Jul 02, 2014 at 01:17:05PM -0500, Sai B wrote:
> I am getting following error while running khmer
> 
> Traceback (most recent call last):
>   File "./interleave-reads.py", line 27, in <module>
>     import khmer
> ImportError: No module named khmer
> Traceback (most recent call last):
>   File "./normalize-by-median.py", line 21, in <module>
>     import khmer
> ImportError: No module named khmer

Hi Sai,

there are three options --

1) install khmer in a virtualenv; see

	http://khmer.readthedocs.org/en/v1.1/install.html#latest-stable-release

This does not require root privileges.

2) install khmer globally, which requires sysadmin privileges; basically,

	pip install khmer

3) run khmer in developer mode, which is what it looks like you're trying to
do.

For this, go to the top level directory within the khmer package or repository,
and type

	make
	export PYTHONPATH=`pwd`

and then everything should work.

best
--titus
-- 
C. Titus Brown, ctb at msu.edu



More information about the khmer mailing list