# working folder
cd /data/www/jbrowse/Auke_202011
	
# Copy a template folder	

# empty the folder data/bed
# empty the folder data/names
# empty the folder data/seq	
# empty the folder data/tracks	

# format gff fna tot genomes
	copy all fna to ./data/genomes
	copy all gff to ./data/genomes
	copy all bed to ./data/bed
	
	
cd /data/www/jbrowse/Auke_202011

# change header to one ID: e.g. >NC_000964.3	
bin/prepare-refseqs.pl --fasta data/genomes/Control.fna
bin/prepare-refseqs.pl --fasta data/genomes/Control_Dxs.fna
bin/prepare-refseqs.pl --fasta data/genomes/MAR_TAG.fna
bin/prepare-refseqs.pl --fasta data/genomes/MAR_TAG_Dxs.fna

# add annotation
bin/flatfile-to-json.pl --gff data/genomes/Control.gff --trackLabel Control --trackType CanvasFeatures
bin/flatfile-to-json.pl --gff data/genomes/Control_Dxs.gff --trackLabel Control_Dxs --trackType CanvasFeatures
bin/flatfile-to-json.pl --gff data/genomes/MAR_TAG.gff --trackLabel MAR_TAG --trackType CanvasFeatures
bin/flatfile-to-json.pl --gff data/genomes/MAR_TAG_Dxs.gff --trackLabel MAR_TAG_Dxs --trackType CanvasFeatures



# make feature searchable
# bin/prepare-refseqs.pl -gff docs/gff/xxxxx.gff
bin/prepare-refseqs.pl -gff data/genomes/Control.gff
bin/prepare-refseqs.pl -gff data/genomes/Control_Dxs.gff
bin/prepare-refseqs.pl -gff data/genomes/MAR_TAG.gff
bin/prepare-refseqs.pl -gff data/genomes/MAR_TAG_Dxs.gff

# add promoter data from TSSer
# bin/flatfile-to-json.pl --bed docs/bed/TSSer.bed --trackType CanvasFeatures --trackLabel TSSerAll

# active the names
bin/generate-names.pl


# make data/tracks.conf file in folder; /data/www/jbrowse/Auke_202011/data
# 1) make or edit the tracks_conf.table, e.g. in Excel
# 2) save the updated tracks_conf.table file
# 3) convert a table direct to a tracks.conf file.
/data/molgentools/tools/jbrowse_table_2_tracks.pl -i tracks_conf.table > tracks.conf

# Optional: Change default spacing between tracks open jbrowse.conf and add the line "view.trackPadding = 7"

# Optional BAM files:
# If BAM is empty, check the genome header name
#/data/molgentools/tools/find_and_replace_single.pl -i MG1363_A.sorted.bam -f 'gi|125622882|ref|NC_009004.1|' -r 'NC_009004.1' -o MG1363_A.sorted.new.bam