Many times the results generated by the bioinformatics programs are either simple text files (tab/comma seperated), pdf files or in some rare cases png/jpeg files. Here we will show you how to view these files without having to download them locally to your machine.
Text files
The text files are the easiest. You can use any of the standard UNIX commands to view them. There are many commands for this purpose such as:
| Command | Purpose | Example | Use cases |
|---|---|---|---|
less |
view file pagewise with more options | less filename |
use -S to avoid line wrapping, you can use arrow keys to scroll |
more |
view file pagewise | more filename |
use less instead |
cat |
catalogs the contents of a file | cat filename |
you can send the contenst of a file to clipboard or to another file using this command |
tac |
reverse of cat, reverses the order of lines | tac filename |
pipe this to less commad to scroll through the file in reverse |
head |
view first few lines of a file | head filename |
use -n option to change the number of lines displayed. -n 20 displays 20 lines |
tail |
view last few lines of a file | tail filename |
use -n option to change the number of lines displayed. -n 20 displays 20 lines |
od |
octal dump of a file | od filename |
use-c options and pipe it through less. You can see non printable characters with this option (like tab, whitespace, newline etc) |
PDF files
Most HPC’s allows X11 forwarding. You can enable this when you are logging in to the remote host using the -X option. For eg.,
ssh -X arnstrm@condodtn.its.iastate.edu
Once logged in, you can now open any GUI interface programs on the remote-host and it appears as a new window in your local machine. Although, there are plenty of program options to open a pdf file, you can almost always find the firefox browser in every machine. This should be sufficient to open a PDF file. To get started, type:
firefox
A new window will open, then go to file » open file » select the pdf file you want to open .
If you don’t find the menu tab, pressing alt + f should bring up the file menu
PNG files
Again, you need X11 forwarding enabled to do this. If your machine has imagemagick module installed, load it:
module load imagemagick
To open any picture files, you can just do:
display filename.png
If you don’t have this program installed, you can try the firefox method. Although, to view png files, you may have to install the addon before you open the file. Addons are easy to add, once the firefox is opened, press ctrl + shift + A, that will open add-ons page (you can also just type about:addons to open this). Search for Perfect View add-on, and add it to your firefox. Now you can open the file normally as you opened the pdf files.