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SJTU-CGM / HUPAN

Human pan-genome analysis pipeline
http://cgm.sjtu.edu.cn/hupan/
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missing config_file (or maker_config) #10

Open sebetso388 opened 4 years ago

sebetso388 commented 4 years ago

Good day,

I am trying to run the genePre command but I cannot find the config_file (or maker_config). Is it an installation/compilation issue?

Thanks

zhqduan commented 3 years ago

Sorry for the later response. The config_file is produced by Maker, and this is a example:

##This file is the configure file using in maker software.
#You can list other parameters at the end of this file according to maker manual
est= #Set of ESTs or assembled mRNA-seq in fasta format.For most options that take a file name, you can supply multiple files using comma (,) seperated lists. i.e. est=est1.fasta,est2.fasta.
protein= #Protein sequence file in fasta format (i.e. from mutiple oransisms)
model_org=Human #Select a model organism for RepBase masking in RepeatMasker
snaphmm= #SNAP HMM file, you can find it in /PATH/to/snap/HMM/ directory.
augustus_species=human #Augustus gene prediction species model
est2genome=1 #Infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no