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choderalab / msm-pipeline

A pipeline for MSMs.
GNU Lesser General Public License v3.0
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Fixing a bug and adding a shell script #6

Closed steven-albanese closed 8 years ago

steven-albanese commented 8 years ago

So, I found a bug where project_name wasn't being passed to plot_sanity_check, which was throwing up an error. Just wanted to merge in the fix for that. I also added pipeline-torque.sh, which is a shell script for running the pipeline on the batch queue on the cluster.

There are some other small changes, like max_iter, which I doubled because 500 steps wasn't enough to converge clustering the WT mTOR kinase domain data, but I don't think that's necessarily a change that needs to be included here. I can revert it, if you'd like

steven-albanese commented 8 years ago

Oh- I also commented out a few lines where the script was trying to pickle some generators, which was giving me an error message as well. They don't appear to be used elsewhere at the moment, but I can revert those as well if wanted

maxentile commented 8 years ago

Thanks for finding and correcting these issues!

Looks good to me.

steven-albanese commented 8 years ago

@maxentile and I noticed a problem where using a path_to_trajs with a wild card would still return only a single trajectory when printing fnames. Seems like using single quotes around the trajectory fixes that problem

jchodera commented 8 years ago

Awesome! Are there any sample plots being generated with this to show what the pipeline is doing so far? If so, I'd love to see them! Maybe share them on the #msm slack channel?

steven-albanese commented 8 years ago

sorry @jchodera, I just saw your comment. The plots being generated here are the same as I showed you when we met earlier today. Maybe we could run the pipeline on a more straightforward case than mTOR to see? I've got it chugging away on an EGFR project over the weekend

steven-albanese commented 8 years ago

Ok this should be ready to merge, I think I've cleaned everything up appropriately!

sonyahanson commented 8 years ago

Thanks for fixing these typos, Steve. I hadn't been able to get the image making scripts to work, yet, so this is great! And yeah the pickling problem is already in issue #2. Will merge! (We can add show plots in a later PR or on Slack.)