https://divingintogeneticsandgenomics.com/tags/bash/ Recent content in Bash on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Fri, 24 Feb 2017 08:44:00 -0800 https://divingintogeneticsandgenomics.com/archive/use-bash-associate-array-to-generate-commands/ Fri, 24 Feb 2017 08:44:00 -0800 https://divingintogeneticsandgenomics.com/archive/use-bash-associate-array-to-generate-commands/ The problem 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 24 samples, and I want to generate pyclone commands for all of them. The solution I usually generate command by bash and then use another bash wrapper to generate pbs files on HPC ((Thanks to @SBAmin). now for each patient, I have two samples. https://divingintogeneticsandgenomics.com/archive/extract-all-kinds-of-archives-on-the-fly-using-extract-command/ Mon, 25 Apr 2016 16:55:00 -0700 https://divingintogeneticsandgenomics.com/archive/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. View this gist on GitHub The extract function can deal with all kinds of archives. I found it is very handy. see it from the original author on github. https://divingintogeneticsandgenomics.com/archive/using-wget-to-download-specific-files-from-ftp-but-avoiding-the-directory/ Wed, 23 Dec 2015 21:09:00 -0800 https://divingintogeneticsandgenomics.com/archive/using-wget-to-download-specific-files-from-ftp-but-avoiding-the-directory/ 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 very versatile command and I just got to know several tricks. When there are many levels of folder, you want to search down to all the folders: -r --recursive Turn on recursive retrieving. -l depth --level=depth Specify recursion maximum depth level depth. https://divingintogeneticsandgenomics.com/archive/ibash-notebook-for-reproducible-research/ Mon, 04 May 2015 20:48:00 -0700 https://divingintogeneticsandgenomics.com/archive/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. Last week, one of my colleagues complained that she forgot how she got the data and processed the data. With a future "ME" in mind, one needs to do extensive documentations of where, when and how you download and process the data, and document the versions of the tools used in the analysis. https://divingintogeneticsandgenomics.com/archive/rename-a-bunch-of-files-with-bash-by-regular-expression/ Thu, 14 Aug 2014 07:44:00 -0700 https://divingintogeneticsandgenomics.com/archive/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 convention. In the protocol it requires fastq files listed as: *001_R1.fastq.gz 001 is the replicate number, it can be 002 or 003 or any number of replicates you have. ( for RNA-seq, sequence as many as biological samples as possible !