Homer error, how to call homer properly in a script? and how to know that it's actually working

Question

[elshaimaa.ali]

!!! HOMER not configured properly!!!! !!! Could not open /gpfs/data01/cbenner/software/homer/.//config.txt !!!

[Kevin Blighe]

Hello, would you answer this question if you were not you? Please, explain a little more what you are trying to do. Also, show the full commands that you are using. Failure to do this will likely mean that nobody will attempt to answer your question.

[yueli7]

Hello, elshaimaa.ali,

How can you figure out this problem?

Thanks in advance!

Yuw

[Ankur B. Sharma]

You should open the findMotifsGenome.pl script and change the path to homer in your system. Hope it helps!

[Ram]

This has already been suggested. Please explain what your answer contributes that previous answers already have not already contributed. Until then, I'm moving your "answer" to a comment.

Answer 1

[Benn]

It is quite well described how to install and configure Homer. Follow the instructions found here, or call Chuck Norris.

Answer 2

[adz]

Despite having tried the installation guide (v4.10, 5-16-2018), I had the same error when executing,

./findMotifsGenome.pl 
Could not open configuration file (/gpfs/data01/cbenner/software/homer/.//config.txt)

I checked perl ../configureHomer.pl and the current base directory for HOMER was ok but still failed.

So, I solved the problem changing two lines in findMotifsGenome.pl and in HomerConfig.pm

use lib "/gpfs/data01/cbenner/software/homer/.//bin";
my $homeDir = "/gpfs/data01/cbenner/software/homer/./";

Hope this helps.

EDIT: It seemed that ./findMotifsGenome.pl worked but due to other dependencies I couldn't run Homer.

EDIT2: a conda environment installing homer is what worked for me.

Regards,
Alicia

[rb56]

HI Alicia, I'm facing something similar as well. Would you mind telling me how you installed a conda environment for homer?

Thanks!

[Ram]

I guess it'd be like setting up any conda environment

conda create -n homer_env -c bioconda homer
conda activate homer_env

[rb56]

Hi Ram,

Thanks for your reply! I'm actually very new to the field of bioinfo and have trouble understanding NGS analysis. I'm trying to run homer for post processing on my directories, to remove out of Bound tags. Here is what the error looks like: https://ibb.co/NyMHdB1 Do you think this is because I didn't set up a conda emvironment?

Thanks in advance!

[Ram]

When you're seeing command line errors, it's best to copy-paste the text and use code formatting. I have not used homer, but it looks like you're missing a resource file, and the tool to create that resource file cannot be executed.

What is the output to

stat /Users/<redacted>/Desktop/Lab/Homer/bin/homerTools

[rb56]

16777224 2415077 -rwxr-xr-x 1 rithika staff 0 2819712 "Nov 5 18:03:30 2019" "Nov 5 18:00:54 2019" "Sep 1 16:13:20 2020" "Nov 5 18:00:54 2019" 4096 5512 0 /Users/Desktop/Lab/Homer/bin/homerTools

[rb56]

I figured out the problem, there was an error in the executable path. Thanks a lot @RamRS