[main]
bg = bg
template_dir = templates
score_dir = score_dists
gene_dir = genes
motif_databases = motif_databases
tools = included_tools/ 

[params]
fraction = 0.2
use_strand = False
abs_max = 1000
analysis = xl
enrichment = 1.5
size = 200
lsize = 500
background = gc,random
cluster_threshold = 0.95
scan_cutoff = 0.9
available_tools = AMD,BioProspector,ChIPMunk,DiNAMO,DREME,GADEM,HMS,Homer,Improbizer,MDmodule,MEME,MEMEW,MotifSampler,Posmo,ProSampler,RPMCMC,Trawler,Weeder,XXmotif,YAMDA
tools = BioProspector,Homer,MEME
pvalue = 0.001
max_time = -1 
ncpus = 12
motif_db = gimme.vertebrate.v5.0.pfm
use_cache = False


[AMD]
bin = AMD.bin
dir = included_tools/

[BioProspector]
bin = BioProspector
dir = included_tools/

[ChIPMunk]
bin = ChIPMunk.sh
dir = included_tools/ChIPMunk

[DiNAMO]
bin = dinamo
dir = included_tools/

[DREME]
bin = dreme-py3
dir = included_tools/

[GADEM]
bin = gadem
dir = included_tools/

[HMS]
bin = hms
dir = included_tools/HMS

[Homer]
bin = homer2
dir = included_tools/

[Improbizer]
bin = ameme
dir = included_tools/

[MDmodule]
bin = MDmodule
dir = included_tools/

[MEME]
bin = meme
dir = included_tools/

[MEMEW]
bin = meme
dir = included_tools/

[MotifSampler]
bin = MotifSampler
dir = included_tools/

[Posmo]
bin = posmo
dir = included_tools/

[ProSampler]
bin = ProSampler
dir = included_tools/

[RPMCMC]
bin = multi_motif_finder
dir = included_tools/

# This section works with trawler as installed by bioconda.
# For other installations set the correct executable name
# as well as the directory.
[Trawler]
bin = trawler
dir = included_tools/

# This section works with weeder as installed by bioconda.
# For other installations set the correct executable name
# as well as the directory.
[Weeder]
bin = weeder2
dir = included_tools/

[XXmotif]
bin = XXmotif
dir = included_tools/

[Yamda]
bin = run_em.py
dir = included_tools/
