Install ea-utils

[sylvie.le.borgne]

Hi, I am new to Bioinformatics and Linux, I have dowloaded ea-utils 1.1.2-537 in my Ubuntu box and unzipped it. I tried to use the fastq-join with my paired reads but the following message appeared:
fastq-joint command not found
Is there something else i need to do to install ea-utils in my box?
Thank you

[Brian Bushnell]

I don't recommend fastq-join; in my tests, it's worse than pretty much every alternative other than Pear.

[GenoMax]

Hi, I am new to Bioinformatics and Linux, I have dowloaded ea-utils 1.1.2-537 in my Ubuntu box and unzipped it. I tried to use the fastq-join with my paired reads but the following message appeared:
fastq-joint command not found
Is there something else i need to do to install ea-utils in my box?
Thank you

Probably not (assuming ea-utils are already compiled). You may need to add execute permissions

$ chmod u+x /path_to/fastq-join

or provide full path to fastq-join as you try to run it

$ /path_to/fastq-join your_R1_file your_R2_file

[sylvie.le.borgne]

Thank you, I tried but it did not work. In the ea-utils folder I have fastq-join.c, I dont know what is the meaning of the letter c....

[GenoMax]

Thank you, I tried but it did not work. In the ea-utils folder I have fastq-join.c, I dont know what is the meaning of the letter c....

That means it is source code that needs to be compiled. There should be a readme-type document included in the source to tell you how to compile the code to make executable files.

Generally a

$ make

in the directory may be all that is needed.

[sylvie.le.borgne]

you mean this:

make home/sylvie/desktop/ea-utils.1.1.2-537/

or make home/sylvie/desktop/ea-utils.1.1.2-537 ?

[GenoMax]

$ cd /home/sylvie/desktop/ea-utils.1.1.2-537
$ make

Good guide for basics of unix for a biologist: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

[LVAndrews]

fastq-join works OK, you just need to relax it because it is so stringent. I use -m 30 -p 30 with good success. Some data is crappier than other data and may need additional grooming before it can be successfully merged.

[bio_informatics]

Late here:
Last I recall installing, ea-utils needed libgsl-dev library to install