stevekm

#!/bin/bash

#~~~ Shell Options ~~~~#
# use some extra shell glob features; turn them on here
# remember whether extglob was originally set, so we know whether to unset it
shopt -q extglob; extglob_set=$?
# set extglob if it wasn't originally set.
((extglob_set)) && shopt -s extglob
# Note, 0 (true) from shopt -q is "false" in a math context.

stevekm

#!/bin/bash

PassList="password1 password2 password3" && OldDir="$(pwd)"
for i in $PassList; do
	for q in $(find . -name "*.rar"); do
		echo "$q"
		NewDir=$(dirname "$q")
		echo -e "\t$NewDir"
		cd "$NewDir"
		~/Downloads/rar/unrar e -p${i} *.rar

stevekm

First method (the hard way)

http://naleid.com/blog/2012/01/17/finding-and-purging-big-files-from-git-history

Second method (easier)

https://help.github.com/articles/removing-files-from-a-repository-s-history/
https://rtyley.github.io/bfg-repo-cleaner/
also see: http://stackoverflow.com/questions/2100907/how-to-remove-delete-a-large-file-from-commit-history-in-git-repository

stevekm

https://help.github.com/articles/duplicating-a-repository/

https://help.github.com/articles/what-happens-to-forks-when-a-repository-is-deleted-or-changes-visibility/

http://stackoverflow.com/questions/16052477/delete-fork-dependency-of-a-github-repository

stevekm

#!/bin/bash

# PROBLEM: want to preseve the terminal output from bowtie2, but also copy the stderr from bowtie into a separate file
# SOLUTION: use `tee` along with some bash stream redirection to copy the stderr stream to a new file AND print it on the terminal


# set files and places
tmp_fastq1="$HOME/projects/SmithLab_PARCLIP/14Q-sample1_R1_mini.fastq"
tmp_fastq2="$HOME/projects/SmithLab_PARCLIP/14Q-sample1_R2_mini.fastq"
tmp_outdir="$HOME/projects/SmithLab_PARCLIP/test_bowtie2"

stevekm

I dunno why this is not readily visible from the main pages:

https://github.com/search/advanced

http://stackoverflow.com/questions/32119877/searching-in-multiple-github-repositories

stevekm

#!/bin/bash

# on OS X, need to install ffmpeg
# so that we can convert FLAC music files
# into mp3 files

# install ffmpeg
brew install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265
brew update && brew upgrade ffmpeg

stevekm

Its already installed:

$ pip install virtualenv
Requirement already satisfied (use --upgrade to upgrade): virtualenv in ./Library/Python/2.7/lib/python/site-packages

But it doesn't work

$ virtualenv
-bash: virtualenv: command not found

stevekm

Anaconda python:
/Users/$USER/anaconda/bin/python

system python
/usr/local/bin/python
/Library/Python/2.7/site-packages/

stevekm

sudo find /media/steve/Orchard/home/steve/ -type f -exec md5sum {} \; > /home/steve/Orchard_files.txt