How to install DASQV?

Question

[biomagician]

Dear all,

I would like to use the DASQV software to scrub pacbio reads. https://github.com/thegenemyers/DASCRUBBER

Does anybody know how to install it?

Thanks.

C.

Answer 1

[h.mon]

git clone https://github.com/thegenemyers/DASCRUBBER
cd DASCRUBBER/
make

[biomagician]

Hi,

Thanks, I've done that. Do you know how I can check that the software was installed? I've tried DASqv --help but the command is not found.

C.

[h.mon]

I am afraid you need to do some command-line learning before you can do bioinformatics on the command-line. See the bash tutorials at Software Carpentry, or do a google search for bash tutorials.

./DASqv

In order to use DASqv instead of ./DASqv, search for "set path bash".

[biomagician]

Thanks. I see. So it seems that this file DASqv is an executable file, which is why I have to run it with ./DASqv.

Thanks.

C.

[h.mon]

You have to run as ./DASqv because its location is not included in the PATH environment variable, and ./DASqv is a relative location which works because I (correctly) assumed you were trying to run it from the same folder you compiled. If you change folder and try ./DASqv, it will not work.

Of course, if DASqv were not an executable file, you would get a "permission denied" error.

[biomagician]

OK, I've added the folder to the path and now I can just use DASqv.