Integrated script

[csmagnano]

Closes #1

The main thing to check is that the runPPA script runs properly when trying to install pgd, and that there's no files I accidentally assumed. I've tested on my machine but it would be good to test on another.

We should also confirm how much of what I added could be tested with Travis, but that is probably okay to do until after the initial release.

This pull request fixes issues #1 and #2.

[agitter]

It looks like make runs successfully for PDG on the Travis server and some executable is built in the expected directory. However, the test command fails with

The command "bash scripts/setupPGD.sh" failed and exited with 255 during .

Have you seen that error message before @csmagnano?

[csmagnano]

I figured out the issue @agitter . The network file was not in the correct format for pgd (it had been converted on my personal computer). I updated the setup script to created a converted network file before testing pgd. This is also a plus as travis is now running the makePGDNet.py script, and being able to run pgd on the converted network is proof it works.

[agitter]

That's great that it all runs in Travis now. Thanks for fixing the graph input. I removed the ls commands I was using for debugging. I'll do a more thorough review and add comments soon.

[agitter]

There a few changes to make before merging and a few other ideas we can discuss. Some of these suggestions can instead be noted in a new issue and wait for a later round of revisions.

I'd like to continue thinking about what data is stored in the repository and what is zipped. Are we being inconsistent by zipping the Reactome .gOut files but not the NetBox predicted .sif files?

[agitter]

This looks good to me. These changes close issue #1.