search

dib-lab / khmer-protocols

Other
19 stars 24 forks source link

[Acceptance] Installing khmer fails, setuptools doesn't exist, need to backport fix from Master #161

Open bocajnotnef opened 9 years ago

bocajnotnef commented 9 years ago

Fix is to use a virtualenv when installing/running khmer:

https://github.com/ged-lab/khmer-protocols/blob/master/mrnaseq/1-quality.txt#L64

(This also makes it easier to re-run the tests on the system without reimaging)

bocajnotnef commented 9 years ago

Correction: This fix doesn't work because (for whatever reason) the virtualenv module doesn't exist.

root@screedaccept:~/khmer-protocols/mrnaseq# python2.7 -m virtualenv env
/usr/bin/python2.7: No module named virtualenv

In this case the solution is to modify the literate-resting instructions to instead include python-setuptools and python-pip in the installed software and to execute the easy_install -U setuptools command.