Install ea-utils

sylvie.le.borgne · 04-21-2015, 07:31 PM

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 · 04-21-2015, 10:45 PM

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

GenoMax · 04-22-2015, 02:00 AM

Quote:

Originally Posted by 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

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

Code:

$ chmod u+x /path_to/fastq-join

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

Code:

$ /path_to/fastq-join your_R1_file your_R2_file

sylvie.le.borgne · 04-22-2015, 04:25 AM

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 · 04-22-2015, 04:34 AM

Quote:

Originally Posted by 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....

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

Code:

$ make

in the directory may be all that is needed.

sylvie.le.borgne · 04-22-2015, 04:41 AM

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 · 04-22-2015, 04:49 AM

Code:

$ 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 · 07-06-2016, 10:43 AM

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 · 07-26-2016, 06:21 AM

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

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04-21-2015, 07:31 PM	#1
sylvie.le.borgne Junior Member Location: Mexico Join Date: Apr 2015 Posts: 3	Install ea-utils 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

04-22-2015, 04:49 AM	#7
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	Code: $ 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

07-26-2016, 06:21 AM	#9
bio_informatics Senior Member Location: USA Join Date: Nov 2013 Posts: 182	Late here: Last I recall installing, ea-utils needed libgsl-dev library to install __________________ Bioinformaticscally calm

04-21-2015, 10:45 PM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	I don't recommend fastq-join; in my tests, it's worse than pretty much every alternative other than Pear.

04-22-2015, 04:25 AM	#4
sylvie.le.borgne Junior Member Location: Mexico Join Date: Apr 2015 Posts: 3	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....

04-22-2015, 04:41 AM	#6
sylvie.le.borgne Junior Member Location: Mexico Join Date: Apr 2015 Posts: 3	you mean this: make home/sylvie/desktop/ea-utils.1.1.2-537/ or make home/sylvie/desktop/ea-utils.1.1.2-537 ?

07-06-2016, 10:43 AM	#8
LVAndrews Member Location: Flagstaff, AZ Join Date: Sep 2012 Posts: 55	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.