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Old 04-21-2015, 07:31 PM   #1
sylvie.le.borgne
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Unhappy 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
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Old 04-21-2015, 10:45 PM   #2
Brian Bushnell
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I don't recommend fastq-join; in my tests, it's worse than pretty much every alternative other than Pear.
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Old 04-22-2015, 02:00 AM   #3
GenoMax
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Quote:
Originally Posted by sylvie.le.borgne View Post
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
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Old 04-22-2015, 04:25 AM   #4
sylvie.le.borgne
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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....
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Old 04-22-2015, 04:34 AM   #5
GenoMax
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Quote:
Originally Posted by sylvie.le.borgne View Post
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.
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Old 04-22-2015, 04:41 AM   #6
sylvie.le.borgne
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you mean this:

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

or make home/sylvie/desktop/ea-utils.1.1.2-537 ?
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Old 04-22-2015, 04:49 AM   #7
GenoMax
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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
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Old 07-06-2016, 10:43 AM   #8
LVAndrews
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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.
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Old 07-26-2016, 06:21 AM   #9
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Late here:
Last I recall installing, ea-utils needed libgsl-dev library to install
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