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@luismts
luismts / GitCommitBestPractices.md
Last active April 27, 2024 14:02
Git Tips and Git Commit Best Practices

Git Commit Best Practices

Basic Rules

Commit Related Changes

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.

@delagoya
delagoya / 00_aws_batch_tes_map.md
Last active February 4, 2020 03:03
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.

Job

@brentp
brentp / README.md
Last active October 12, 2023 15:21

Linkage Disequilibrium Calculation

This is complete taken from Ryan D on biostar: http://www.biostars.org/p/2909/#16419

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.

@radaniba
radaniba / enrichment.R
Last active October 13, 2015 08:48
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
sink("log",append=FALSE,type=c("output","message"),split=FALSE)
library(GOstats)
library(EMA)
library(fdrtool)
library(org.Pt.eg.db)
Args <- commandArgs();
UNIV <- Args[6]
#GL <- Args[5]
@misterbrownlee
misterbrownlee / jenkins-notes.md
Created September 12, 2012 18:10
Jenkins setup

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.

Install Jenkins Plugins

@jtriley
jtriley / config
Created August 9, 2012 15:47
Example StarCluster plugin that tags all instances based on tags specified in the config
# This is an example config that assumes tagger.py is either in
# $HOME/.starcluster/plugins or lives somewhere in your $PYTHONPATH
[plugin tagger]
setup_class = tagger.TaggerPlugin
# add as many key=value pairs as you like separated by ','
tags = 'mykey=myvalue, mykey2=myvalue2'
[cluster default]
...