Creating config file

The script requires a config file that contains filepaths, title page, organism name and colors of the page. You can edit the following example based on your filepaths results.

---

organism_name

The parameter organism_name defines the directories and coordinates to application results like:

organism_name=Curtobacterium

So the result directories should be something like:
Curtobacterium_Services
Curtobacterium_Website

fasta_dir

Set directory that storage fasta files from the sequences, the directory gonna be created in both applications(Services and Website) in root directory

fasta_dir=seq

aa_fasta_dir

Set directory that storage amino acids fasta files from the sequences, the directory gonna be created in both applications(Services and Website) in root directory

aa_fasta_dir=orfs_aa

nt_fasta_dir

Set directory that storage nucleotidic fasta files from the sequences, the directory gonna be created in both applications(Services and Website) in root directory

nt_fasta_dir=orfs_nt

infernal_output_file

Set the prefix name of infernal output files
infernal_output_file=infernal

infernal_output_file

Set the prefix name of infernal output files
infernal_output_file=infernal

alienhunter_output_file

Set the prefix name of alienhunter output files

alienhunter_output_file=alienhunter

reports_global_analyses

Set all directories to be used in Global Analyses reports page (all reports should be defined also in JSON file).
At this moment, because of an error, all filepaths should reference a file that can not exists, but must reference a file inside of the directory

reports_global_analyses=/home/wendelhlc/teste_database/upload_xml/output_dir/go_report/go_mapping.html;/home/wendelhlc/teste_database/upload_xml/output_dir/eggnog_report/classes.html;/home/wendelhlc/teste_database/upload_xml/output_dir/kegg_report/classes.html;/home/wendelhlc/teste_database/upload_xml/output_dir/kegg_organism_report/classes.html

report_feature_table_submission_dir

Set genbank reports filepath to be presented in Downloads page
The link should exist in JSON file

report_feature_table_submission_dir = /home/wendelhlc/teste_database/upload_xml/output_dir/genbank_report

report_feature_table_artemis_dir

Set artemis reports filepath to be presented in Downloads page
The link should exist in JSON file

report_feature_table_artemis_dir = /home/wendelhlc/teste_database/upload_xml/output_dir/artemis_report

report_gff_dir

Set GFF reports filepath to be presented in Downloads page
The link should exist in JSON file

report_gff_dir = /home/wendelhlc/teste_database/upload_xml/output_dir/gff3_dir

TCDB_file

Set TCDB file data

TCDB_file=/usr/local/genome/databases/TCDB/TCDB_ID_list

ko_file

Set kegg filepath

ko_file= /usr/local/genome/databases/kegg/ko/ko

homepage_text_file

Set the filepath to JSON file with the data to be used in page result

homepage_text_file = /home/wendelhlc/teste_database/upload_xml/curtobacterium.json

homepage_title

Set homepage title

homepage_title = "<i>Epicoccum nigrum</i> genome project"

homepage_image_organism

Set image organism to be presented in homepage

homepage_image_organism = /home/wendelhlc/Imagens/curtobacterium.jpg

filepath_log

Set filepath log

filepath_log = /home/wendelhlc/teste_database/upload_xml/epicoccum/output/report_html_db.log

component_name_list

Set component list

component_name_list = annotation_trf.pl;annotation_trna.pl;annotation_alienhunter.pl;annotation_infernal.pl;annotation_rnammer.pl;annotation_transterm.pl;annotation_rbsfinder.pl;annotation_bigpi.pl;annotation_predgpi.pl;annotation_tcdb.pl;annotation_phobius.pl;annotation_tmhmm.pl;annotation_signalP.pl;annotation_blast.pl;annotation_rpsblast.pl;annotation_interpro.pl;annotation_orthology.pl;annotation_pathways.pl;annotation_mreps.pl;annotation_glimmer3.pl;annotation_hmmer.pl;annotation_dgpi.pl;upload_prediction.pl

annotation_dir

Set path to annotation directory (where you can find results of annotation components)

annotation_dir=/home/wendelhlc/teste_database/upload_xml/epicoccum/output

filepath_assets

Set filepath for assets.tar.gz file, you can download here filepath_assets=/home/wendelhlc/git/report_html_db/report_html_db/assets.tar.gz

Colors parameters

The following parameters can be used to set colors of the page:

color_primary = "#94618e"
color_accent = "#94618e"
color_primary_text = "#FFF"
color_accent_text = "#FFF"
color_menu = "#49274A"
color_background = "#F8EEE7"
color_footer = "#F4DECB"
color_footer_text = "#333"

In config file example exists 10 sets of colors available, you're free to change any of those parameters