sbamin

This gist I write, because I couldn't find step by step instructions 
how to install and start postgresql locally and not globally in the
operating system (which would require sudo).

I hope, this will help especially people new to postgresql!

####################################
# create conda environment
####################################

sbamin

The fastest remote directory rsync over ssh archival I can muster (40MB/s over 1gb NICs)

This creates an archive that does the following:

rsync (Everyone seems to like -z, but it is much slower for me)

• a: archive mode - rescursive, preserves owner, preserves permissions, preserves modification times, preserves group, copies symlinks as symlinks, preserves device files.
• H: preserves hard-links
• A: preserves ACLs

sbamin

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

sbamin

#!/usr/bin/env Rscript

# modified from a script by:
# Eric Vallabh Minikel
# https://gist.github.com/ericminikel/8428297
# example of how to use optparse in R scripts

# usage: ./exampleRScript1.r -a thisisa -b hiagain
#        ./exampleRScript1.r --avar thisisa --bvar hiagain