You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Here is a script for gene set enrichment over KEGG, the perl script serves as automation for the analysis of several gene set files inside a directory, the R script does the analysis itself using bioconductor GOStats package. Look inside the perl script
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Example StarCluster plugin that tags all instances based on tags specified in the config
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
A mapping of the GA4GH Task Execution Service API schema to AWS Batch
Map of Task Execution Service (TES) to AWS
This document is an overview of how concepts from TES map to concepts in AWS Batch.
AWS Batch - Basic Concepts
AWS Batch ("Batch") has a few basic concepts that need to be understood before we can make a comparison to concepts in TES. Some relate directly to TES and others do not.
It takes a region in a format like "chr2:1234-3456".
If an rs number is specified after the region, it will output
the R^2 for every SNP in that region with the requested SNP;
otherwise, it is all-vs-all.
I just had to set up Jenkins to use GitHub. My notes (to myself, mostly):
Detailed Instructions
For setting up Jenkins to build GitHub projects. This assumes some ability to manage Jenkins, use the command line, set up a utility LDAP account, etc. Please share or improve this Gist as needed.
A commit should be a wrapper for related changes. For example, fixing two different bugs should produce two separate commits. Small commits make it easier for other developers to understand the changes and roll them back if something went wrong.
With tools like the staging area and the ability to stage only parts of a file, Git makes it easy to create very granular commits.
Commit Often
Committing often keeps your commits small and, again, helps you commit only related changes. Moreover, it allows you to share your code more frequently with others. That way it‘s easier for everyone to integrate changes regularly and avoid having merge conflicts. Having large commits and sharing them infrequently, in contrast, makes it hard to solve conflicts.