YeoLab/gscripts — pull request #3 by olgabot (2013-07-15 23:43:40+00:00)
Title: Made qtools more Pythonic and can now import Submitter via `from gscripts.qtools import Submitter`

Also removed `qtools.py` from `gscripts/general/qtools.py`. It's now in `gscripts/qtools/_Submitter.py` and `gscripts/qtools/__init__.py` just has:
```from _Submitter import *```

The Submitter function also had a few bugs for submitting to PBS vs SGE, which have (hopefully) all been fixed.

Some other things:
* Added python command-line submitters (with documented command line flags! and usage when you say `-h`!) for miso jobs (doesn't work on TSCC yet but this may be because of the way my virtualenv paths are configured
* I added the python command-line submitters such as `submit_miso_index_gff.py` and `submit_miso_pipeline.py` to the `scripts` list in `setup.py`, and they get added to my path, but when I do `python setup.py clean ; python setup.py build; python setup.py install`, they are only phantoms:

```
Traceback (most recent call last):
File "/home/obotvinnik/obot_virtualenv/bin/submit_miso_pipeline.py", line 5, in
pkg_resources.run_script('gscripts==0.1.1', 'submit_miso_pipeline.py')
File "/home/yeo-lab/software/python_packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
File "/home/yeo-lab/software/python_packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1201, in run_script
pkg_resources.ResolutionError: No script named 'submit_miso_pipeline.py'
```

So I'm not sure what's going on here. Maybe I'm referencing them incorrectly or not exporting them right. It's probably relevant that to even get my `virtualenv` packages selected before the `/home/yeo-lab/software/python_packages` stuff, I had to do `export PYTHONPATH=~/obot_virtualenv/lib/python2.7/site-packages`, and there's no `numpy` or `scipy` there, only in `yeo-lab` stuff. Any thoughts?