Motivation Be able to check the sha256 sums on the files downloaded from internet Installation Copy the script file into a Scripts folder in your Home directory (at the same level as Documents Downloads etc.) Make the file executable sudo chmod a+x hash-check_sha256 Add the Scripts into path in your ~/.bashrc file by adding a following line at the end PATH="$HOME/Scripts:$PATH" Add the alias hash-check into the aliases into the ~/....

download in pdf format Status: in progress Motivation Use the multicore performance to improve processing of bioinformatics data Resources Ole Tange 2018 excellent book [link to biostars handbook](link to be added) man pages of parallel Simple examples and syntax Crate example files seq 5 | parallel seq {} '>' example.{} Supply one set of arguments to the parallel Count lines example.1 example.2 … example.N parallel wc -l ::: example.* Supply two or more set of arguments to the parallel to process all combinations parallel echo ::: red green ochre ::: fox parrot fish Use the name of the argument in the command parallel echo counting {}';' wc -l {} ::: example....

How to manage versions of documents and scripts from the command line. What is a work tree, staging, and commiting?. How can I go back to a previous version of a file? How to branch to test new variant without losing the functional version, how to tag the version. How to push to GitHub from the command mode using ssh authorization. Resource ProGit book link first three chapters are sufficient....

download as pdf How to set up infrastructure for ChIP-seq analysis using the Biostars Handbook 2nd edition according to Ming Tangs Guide. Setting up the folder structure Go to the directory for ChIP-seq with your analysis cd ~/work/ChIP-seq_<analysis-name> mkdir {data,results,scripts,software} mkdir -p results/{bams,peaks,fastqc,motifs} cd data Download data Get the annotation list from the sra run selector IDs.txt Prefetch and convert files to fastq Go into the ~/work/ChIP-seq_/data time parallel -j 10 'prefetch {}' :::: IDs....

Upgrading HP Z600 Resources in general BIOS version sudo dmidecode -s bios-version 786G4 v03.54 newest bios from support page link sp85652.tgz downloaded in installation folder on Asus laptop CPUs Bought two XEON X5675 processors RAM Decided to go with 96GB of RAM, bought 6x this 16GB stick: DDR3L 1333MHz PC3L-10600 2Rx4 1.35V ECC RDIMM SYSTEM Will install ubuntu 24.04 Remote desktop Remote desktop can be used to not only work on the remote computer, but also copy clipboard and normal files between the remote computer and your local computer...

Terminal colour codes link to wiki page of colours .bashrc # set case insensitivity for the terminal bind "set completion-ignore-case on" # set vim motions on set -o vi .vimrc " set numbering of lines to relative set relativenumber " set formatoptions-=r " set textwidth=80 " if you want to reformat the document, go to start of document and type gqG " set moving up and down centered on the screen nnoremap <C-d> <C-d>zz nnoremap <C-u> <C-u>zz " set the cursor in different modes to be different let &t_EI ="\e[2 q" " block in edit mode let &t_SI ="\e[1 q" " blinking block in insert mode let &t_SR ="\e[3 q" " block in replace mode " set leader to space let mapleader = " " " clear all registers command!...

Extracting relevant columns from csv and tab delimited files. Download as a pdf Exemplary workflow for quick look of papers from pubmed “similar or cited by” Download the citation/similar articles in csv format from pubmed Check the number of lines in the file wc -l file.csv See the names of columns of the file csvcut -n file.csv Create an output for a quick visual check with title and doi, most recent first Option 1: for the output in terminal, comma separated...

Stream editor (sed) edits text files without opening them. Most often, the editing would be a replacement of one character or word by another. This way a delimiter of a csv file can be changed from comma to semicolon, name of a person can be replaced throughout the text. But that is just a beggining; sed has much more to offer: The “word” can be a regular expression making it super flexible The lines where this replacement will be done, can be specified by their line number, range, or content Taken togehter, sed helps to delete, replace, and append characters, words, lines or whole files....

Command line utility ffmpeg, dedicated to different transformations of video, is one of the tools which genuinly feel like magic. ffmpeg download link can do a lot, so it is no surprise that the documentation is overwhelming. Below are some usecases so that I do not have to search for them again and again. Dowload this document as a pdf Use cases Play first 20 sec of multiple videos I downloaded several lectures, but not sure how they go one after another, the sequential number of the lecture appears in first 20 sec of the video....

Setting in .bashrc awk defaults to working with whitespace, not with commas, better ot set the comma as an field separator, and otuput field separator and name this modification awkc. Add this to ~/.bashrc # make a csv specific awk alias awkc='awk -F, -v OFS=,' Split a csv file into multiple files based on 7th column awk -F',' 'NR==1{h=$0; next} { f = $7 ".csv" if (!(f in seen)) { print h > f seen[f] } print >> f }' input....