HISAT2 download

GNU/Linux-Ubuntu 
use *pwd* and check your location! 
4. HISAT2 
> wget  https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download -O hisat2.zip #When you run this command, wget will download the file from the specified URL and save it as hisat2.zip in your current directory.
> unzip hisat2.zip                             #after ls and you must see 'hisat2-2.2.1' file
> ls hisat2-2.2.1/ or ls hisat2-2.2.1/hisat2   #you can check your hisat2 file
> mkdir -p AppFiles/hisat2                     #Create AppFiles and collect all applications file in this "AppFiles".
> mv -v hisat2-2.2.1 AppFiles/hisat2           #Move hisat2-2.2.1 to hisat2 AppFiles
> chmod +x AppFiles/hisat2                     #chmod: This is the command used to change file permissions.
                                               #+x: This option tells chmod to add the executable permission.
                                               #hisat2: This specifies the file path of the hisat2 file within the directory.
> pwd
> export PATH=$PATH:/home/aysegul/AppFiles/hisat2      #Don't forget change your local location

#If you want, you can copy the .bashrc file, open this file use nano function, and paste this PATH to an empty place at the bottom of this file and save it,
use this code: 
> cp .bashrc bashrc.original                           #cp: This is the command used to copy files or directories.
                                                       #.bashrc: This is the name of the file you want to copy. It's typically a configuration file for the Bash shell. 
                                                       #bashrc.original: This is the name of the backup file you want to create. It will contain a copy of the original .bashrc file.
> nano .bashrc
> paste 'export PATH=$PATH:/home/aysegul/AppFiles/hisat2'
save Ctrl+O, enter and for exit use: Ctrl+X