Aaron Gu
Aaron Gu
Can there be a notification upon failure saying something like "Did you mean to use 'wgbs' instead of 'WGBS'"?
This has been mostly addressed with commit d6674fc084b0805aedd3337ef0bd7c1adfeab669. Cut and merge are the two slowest operations now, but can still complete reasonably quickly. I'll keep this issue open to see...
Also see #11
Well, my change to creating new regions and dropping old regions didn't help improve the shift performance by much. I think the slow part about shift is in the Pandas...
New idea: 1. take a subset of the Dataframe, which will be the rows to modify 2. use an `apply` function on the start and end columns to get shifted...
I am just using `looper run project_config.yaml`
I set up a PEP project for my bedshift code to generate the 100 samples for every parameter combination. I followed the PEP and looper tutorials pretty smoothly until it...
Here's an example of a .sub file: ``` #!/bin/bash #SBATCH --job-name='bedshift_run_add1' #SBATCH --output='looper_output/submission/bedshift_run_add1.log' #SBATCH --mem='{MEM}' #SBATCH --cpus-per-task='{CORES}' #SBATCH --time='{TIME}' #SBATCH --partition='standard' #SBATCH -m block #SBATCH --ntasks=1 #SBATCH --open-mode=append echo 'Compute...
Got it, thanks! Is there a way to make it easier to find that section of documentation? The order I went through the docs was Introduction > Defining a Project...