Bash

use bash associate array to generate commands

I am running pyclone recently to determine the clonality of our collected tumor samples. It needs tumor purity (estimated from sequenza) for input. I have…

extract all kinds of archives on the fly using extract command

If you are tired of remembering (googling) how to extract different kinds of archives like me, use this gem I found.

Using wget to download specific files from ftp but avoiding the directory structure

I want to download some files from a ftp site, and I only want to download some files with names matching a pattern. How can I do it?\ Use wget ! It is a…

IBash Notebook for reproducible research

I use command line a lot. It is awesome for data processing, text data formatting and even exploratory data analysis.

rename a bunch of files with bash by regular expression

I am at the MSU NGS 2014 course. My colleague wanted to follow the khmer protocol with his own data, but one of the steps has to use a certain file name…