Problem running trim_galore and cutadapt

[jadon]

I am being automatically logged out of trim_galore and cutadapt as soon as I open them in the terminal.

Cutadapt
[
cutadapt: error: At least one parameter needed: name of a FASTA or FASTQ file.
logout
]

Trim Galore
[
Please provide the filename(s) of one or more FastQ file(s) to launch Trim Galore!

USAGE: 'trim_galore [options] <filename(s)>' or 'trim_galore --help' for more options

logout
]

Has anyone ran into this problem or does anyone have any idea why this is happening? I am using Mac OS X 10.9

Any help is appreciated.

[GenoMax]

Are you using trim galore as shown in the user guide (page 5): http://www.bioinformatics.babraham.a...ide_v0.2.4.pdf

Can you post the command you are issuing?

[dpryan]

That's extremely unusual. Assuming you're not root on that system, you might ask the sysadmin WTF is going on.

[GenoMax]

Trim galore/cutadapt do not have a graphical user interface that allows one to run them by double-clicking the icon (I think that is what you are doing). These programs have to be run on the command line (in a "terminal"). Here is a simple guide on how to use the command line on OS X: http://blog.teamtreehouse.com/introd...x-command-line

[jadon]

Yeah that was the problem, I was opening them directly instead of through the terminal. Thanks for the help.