Setting Alias or PATH variable

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Basics of altering the `~/.bashrc` or `~/.bash_profile` file

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Reason

Often times you may need to run a command from a downloaded piece of software, but would like to avoid the inconvience of including the entire path as part of the command. This can be avoided by updating you ~/.bashrc or ~/.bash_profile with either an alias for a particular pathway/file or by amending you $PATH variable to include the specific folder in which your command is located. The later may be particularly useful if the software contains multiple commands you need to call.

Disclaimer

• This tutorial is intended for those that are using bash shell, so if you are working with another shell (i.e. zsl) these specific files we are modifying will be different.

Creating an Alias

Open your bashrc (or bash_profile) file

nano ./bash_profile

Add an alias

alias new_command="/absolute/path/to/actual/command.sh"

Source your bash file (or restart terminal) to make the changes active

source(~/.bash_profile)

Updating your $PATH variable

Open your bashrc (or bash_profile) file

nano ./bash_profile

Add to existing items of $PATH

PATH=$PATH:/path/to/folderWith/Commands

• Generally good idea to add this line after where you see other $PATH variable entries, but before the line that exports the entries (i.e. export PATH)

Source your bash file (or restart terminal) to make the changes active

source(~/.bash_profile)

Example of a bash_profile file

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
        . ~/.bashrc
fi

# User specific environment and startup programs

PATH=/shared_lab/scripts:/shared_lab/scripts/bin:$PATH:$HOME/.local/bin
PATH=$PATH:/shared_lab/20180226_RNAseq_2017OAExp/RNA/scripts/salmon_scripts/
PATH=$PATH:/shared_lab/20180226_RNAseq_2017OAExp/RNA/scripts/software/RSEM/RSEM-1.3.1
PATH=$PATH:/shared_lab/20180226_RNAseq_2017OAExp/RNA/scripts/software/gffread
PATH=$PATH:$HOME/downey-wall.a_remote/scripts
PATH=$PATH:/shared_lab/20180226_RNAseq_2017OAExp/RNA/scripts/software/gffcompare
PATH=$PATH:/shared_lab/20180226_RNAseq_2017OAExp/RNA/scripts/STAR_scripts
PATH=$PATH:/home/downey-wall.a/software/hisat2-2.1.0
PATH=$PATH:/home/downey-wall.a/software/Bismark-0.22.1
PATH=$PATH:/home/downey-wall.a/software/TrimGalore-0.6.0
PATH=$PATH:/shared_lab/20180226_RNAseq_2017OAExp/DNAm/scripts
PATH=$PATH:/usr/local/programs/R/3.6.0/bin
PATH=$PATH:/home/downey-wall.a/software/bowtie2-2.3.5.1-linux-x86_64
PATH=$PATH:/home/downey-wall.a/downey-wall.a_remote/software
export PATH

# Aliases
alias python='/home/downey-wall.a/python_3.5.2/bin/python3.5'