sbamin

Peek into HPC Helix Health

Samir B. Amin, @sbamin

hpcinfo is a primary script to check status of Helix HPC at JAX GM. Optimized for VerhaakEnv but should work for most users.

Place both hpcinfo and check_helix_health in either ${HOME}/bin/ or directory which is under HPC $PATH.

sbamin

How-to access journal articles via JAX EZProxy

Does not require VPN

• For chrome browser, install EZProxy Redirect extension

https://chrome.google.com/webstore/detail/ezproxy-redirect/gfhnhcbpnnnlefhobdnmhenofhfnnfhi

• Under options for ezproxy extension, choose following custom URL:

sbamin

backup dotfiles

• Following will copy all of dot ~/. files and directories (including its contents) directly underneath home directory.
• To avoid copying cache and other local configs, e.g., that of web browser, java apps, etc., preferably query directory size tool under entire home $HOME/, using ncdu $HOME of similar tool.
• Exclude all those large directories using rsync --exclude=.local --exclude=.cache format
• Avoid rsync password, ssh keys, .bash_history, etc. if you are uploading to github, etc.
• rsync home dotfiles and configs as follows:

# in your local machine

sbamin

source 'https://rubygems.org'

gem 'nokogiri', '= 1.6.8.1'

group :jekyll_plugins do
gem 'github-pages', '>= 127'
end

group :jekyll_misc_plugins do
gem 'jekyll-compose', '>= 0.4.1'

sbamin

#!/bin/bash

## Wrapper to interact with NCBI SRA using aspera ascp command line interface
## v 2.5 | 04/2017
## @sbamin

# More info: http://download.asperasoft.com/download/docs/ascp/2.7/html/

# usage
show_help() {

sbamin

# User specific aliases and functions
# JAX Helix - HPC
# v 2.2.3 | 03-17 | @sbamin

alias ll='ls -alhF'
alias la='ls -A'
alias l='ls -CF'
alias df='df -H'
alias du='du -ch'
alias cd..='cd ..'

sbamin

Plot using mermaid

http://knsv.github.io/mermaid

[Link to this plot](https://knsv.github.io/mermaid/live_editor/#/view/Z3JhcGggVEI7CnN1YmdyYXBoIE5PUk1BTApOUl9MMV9SMS0tPnxCV0EgTUVNfE5SX0JBTV8xCk5SX0wyX1IxLS0-fEJXQSBNRU18TlJfQkFNXzIKTlJfTDFfUjItLT58QldBIE1FTXxOUl9CQU1fMQpOUl9MMl9SMi0tPnxCV0EgTUVNfE5SX0JBTV8yCgpOUl9CQU1fMS0tPnxNQVJLIERVUHxOUl9CQU1fMS5tZHVwW3BlciBsYW5lIG1kdXAgYmFtXQpOUl9CQU1fMi0tPnxNQVJLIERVUHxOUl9CQU1fMi5tZHVwW3BlciBsYW5lIG1kdXAgYmFtXQoKc3R5bGUgTlJfQkFNLm1kdXAgZmlsbDojZjlmLHN0cm9rZTojMzMzLHN0cm9rZS13aWR0aDo0cHg7CgpOUl9CQU1fMS5tZHVwLS0-fE1BUksgRFVQfE5SX0JBTS5tZHVwKG1lcmdlZCBiYW0gd2l0aCBwZXIgbGFuZSBSR0lEICYgbWFyayBkdXAgb24gbWVyZ2VkIGJhbSkKTlJfQkFNXzIubWR1cC0tPnxNQVJLIERVUHxOUl9CQU0ubWR1cAoKTlJfQkFNLm1kdXAtLi0-fElOREVMIFJFQUxJR04gPGJyPiBmb3IgbGVnYWN5IHBpcGVsaW5lfE5SX21kdXAuaW5kZWwuYmFtCgpzdHlsZSBOUl9tZHVwLmluZGVsLnJlY2FsLmJhbSBmaWxsOiNmOWYsc3Ryb2tlOiMzMzMsc3Ryb2tlLXdpZHRoOjRweDsKTlJfbWR1cC5pbmRlbC5iYW09PT58QlEgU1J8TlJfbWR1cC5pbmRlbC5yZWNhbC5iYW0obWR1cC5pbmRlbC5yZWNhbC5iYW0pCmVuZAoKc3ViZ3JhcGgg

sbamin

sbamin

--------------------------------------------------------------------------------
The Genome Analysis Toolkit (GATK) v3.1-0-g72492bb, Compiled 2015/01/21 17:10:56
Copyright (c) 2010 The Broad Institute
For support and documentation go to http://www.broadinstitute.org/gatk
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
usage: java -jar mutect-1.1.7.jar -T <analysis_type> [-args <arg_file>] [-I <input_file>] [-rbs <read_buffer_size>] [-et 
       <phone_home>] [-K <gatk_key>] [-tag <tag>] [-rf <read_filter>] [-L <intervals>] [-XL <excludeIntervals>] [-isr 
       <interval_set_rule>] [-im <interval_merging>] [-ip <interval_padding>] [-R <reference_sequence>] [-ndrs] [-maxRuntime 
       <maxRuntime>] [-maxRuntimeUnits <maxRuntimeUnits>] [-dt <downsampling_type>] [-dfrac <downsample_to_fraction>] [-dcov 

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