annotatePeaks.pl Homer Issue

Software and Programming
1

Hello, I’m trying to annotate ChIP-seq peaks using Homer.
Here is my code:

module load gcc/8.3.0
module load homer/4.9.1

H3cl="/project/juddrice_462/bweekley/chipacMNasemerged/analysis/100bpSW/D5K14AllH3andK14diff_HOMER.bed"
genome="/scratch/bweekley/bhw/genomes/mm10_for_heatmap/refTSS_v3.1_mouse_coordinate.mm10.bed"
output="/project/juddrice_462/bweekley/chipacMNasemerged/analysis/homer"

annotatePeaks.pl $H3cl $genome > $output/D5K14AllH3andK14diff_HomerRefSeqAn.bed

And the error I get:
“Could not open configuration file (/spack/apps/linux-centos7-x86_64/gcc-8.3.0/homer-4.9.1-xn6ioaqj6ouc26olaqrqzqtz44he7tty/lib/homer//config.txt)”

Not sure how to get around this. It seems if I try to use other Homer .pl operators they work just fine. Any and all help is greatly appreciated.
Ben

2

@bweekley I installed the mm10 package, and now there is a config.txt file. You can see other available packages with the command perl $HOMER_ROOT/lib/homer/configureHomer.pl -list. Let us know if there are others that you need. You can try your command again once the changes are synced over later today.