<commit_before>#!/bin/bash
#AUTHOR: <NAME> {<EMAIL>}
#Date: 2015-08-07

PYTHON_PATH=python3.4
apricot_path=$1
apricot_lib= $apricot_path/apricotlib ##provide full path where you have cloned/save APRICOT from git
apricot_db=$2 #apricot_db_path ##provide full path where you want to store the data
apricot_flatfiles=bin/reference_db_files/

main(){
        create_db_path
        
        ###DATABASES###
        create_cdd_inpath
        check_and_download_cdd
        create_interpro_inpath
        check_and_download_interpro
        ###ANNOTATION TOOLS###
        install_raptorx
        install_psortb
        
        ###FLAT-FILE DATA###
        create_flatfile_path
        ###CDD-MODULES###
        create_cdd_flatfiles_inpath
        check_and_download_cdd_flatfiles
        ###InterProScan-MODULES###
        create_interpro_flatfiles_inpath
        check_and_download_interpro_flatfiles
        uniprot_species_to_taxid
        ######PDB-MODULES####
        create_pdb_inpath
        download_uniprot_map
        download_pdb_sec_str
        sort_and_format_pdb_data
        ###Other-requirements###
        get_pfam_domain_file
        get_blast_executables
        ontology_mapping_to_domains
        get_biojs_dependencies
        get_clustalw
} 

create_db_path(){
    for FOLDER in $apricot_db/apricot_db_and_tools
        
    do
        if ! [ -d $apricot_db/apricot_db_and_tools ]
        then
            mkdir -p $apricot_db/$FOLDER
        fi
    done
    for FOLDER in conserved_domain_database \
        interpro psortb raptorx nr
    do
        if ! [ -d $apricot_db/$FOLDER ]
        then
            mkdir -p $apricot_db/$FOLDER
        fi
    done
}
<commit_msg>Update apricot_complete_db_tool.sh<commit_after>#!/bin/bash
# AUTHOR: <NAME> {<EMAIL>}

PYTHON_PATH=python3.4
apricot_path=$1
apricot_lib= $apricot_path/apricotlib   ## provide full path where you have cloned/save APRICOT from git
apricot_db=$2                           ## apricot_db_path ##provide full path where you want to store the data
apricot_flatfiles=bin/reference_db_files/

main(){
        create_db_path
        
        ### DATABASES ###
        create_cdd_inpath
        check_and_download_cdd
        create_interpro_inpath
        check_and_download_interpro
        ### ANNOTATION TOOLS ###
        install_raptorx
        install_psortb
        
        ### FLAT-FILE DATA ###
        create_flatfile_path
        ### CDD-MODULES ###
        create_cdd_flatfiles_inpath
        check_and_download_cdd_flatfiles
        ### InterProScan-MODULES ###
        create_interpro_flatfiles_inpath
        check_and_download_interpro_flatfiles
        uniprot_species_to_taxid
        ### PDB-MODULES ###
        create_pdb_inpath
        download_uniprot_map
        download_pdb_sec_str
        sort_and_format_pdb_data
        ### Other-requirements ###
        get_pfam_domain_file
        get_blast_executables
        ontology_mapping_to_domains
        get_biojs_dependencies
        get_clustalw
} 

create_db_path(){
    for FOLDER in $apricot_db/apricot_db_and_tools
        
    do
        if ! [ -d $apricot_db/apricot_db_and_tools ]
        then
            mkdir -p $apricot_db/$FOLDER
        fi
    done
    for FOLDER in conserved_domain_database \
        interpro psortb raptorx nr
    do
        if ! [ -d $apricot_db/$FOLDER ]
        then
            mkdir -p $apricot_db/$FOLDER
        fi
    done
}

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