| class DivideAndSlurm(object): | |
| """ | |
| DivideAndSlurm is a class to handle a map-reduce style submission of jobs to a Slurm cluster. | |
| Add a particula task to the object (though a specific function) and it will divide the input data | |
| into pools, which will be submitted (use the submit() function) in parallel to the cluster. | |
| Tasks can also further process its input in parallel, taking advantage of all processors. | |
| """ | |
| def __init__(self, tmpDir="/fhgfs/scratch/users/user/", logDir="/home/user/logs", queue="shortq", userMail=""): | |
| super(DivideAndSlurm, self).__init__() |
| # borrowed from here: https://gist.github.com/dan-blanchard/7045057 | |
| # lint it here: http://lint.travis-ci.org/ | |
| language: python | |
| python: | |
| - 2.7 | |
| notifications: | |
| email: false | |
| # whitelist | |
| branches: |
| Interactive Visualization of CyTOF Data | |
| ======================================================== | |
| ```{r setup, echo=FALSE} | |
| library(rgl) | |
| knit_hooks$set(webgl = hook_webgl) | |
| opts_knit$set(upload.fun = imgur_upload, base.url = NULL) # upload all images to imgur.com | |
| ``` | |
| This report produces a 3D visualization of the CD8+ T-cell subsets from [Newell et al. (2012)](http://www.ncbi.nlm.nih.gov/pubmed/22265676) using principal components analysis (PCA). |
Custom recipe to get OS X 10.9 Mavericks running from scratch, setup applications and developer environment. I use this gist to keep track of the important software and steps required to have a functioning system after a semi-annual fresh install.
The software selected is software that is "tried and true" --- software I need after any fresh install. I often install other software not listed here, but is handled in a case-by-case basis.