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#*************************************************************
#Global settings
#*************************************************************
#*************************************************************
#The full path to the cgview_comparison_tool directory. [Path].
comparison_tool = $CCT_HOME
#The location of java. [Path].
java = java
#The location of NCBI's blastall. [Path].
blastall = blastall
#The location of NCBI's formatdb. [Path].
formatdb = formatdb
#The location of Perl. [Path].
perl = perl
#*************************************************************
#*************************************************************
#Internal settings
#*************************************************************
#*************************************************************
seq_split = $comparison_tool/lib/scripts/sequence_to_multi_fasta/sequence_to_multi_fasta.pl
local_blast = $comparison_tool/lib/scripts/local_blast_client/local_blast_client.pl
get_cds = $comparison_tool/lib/scripts/get_cds/get_cds.pl
get_orfs = $comparison_tool/lib/scripts/get_orfs/get_orfs.pl
assign_cogs = $comparison_tool/lib/scripts/assign_cogs/assign_cogs.pl
cogs_files = $comparison_tool/cog_db
whog_file = $cogs_files/whog
myva_file = $cogs_files/myva
cgview_xml_builder = $comparison_tool/lib/scripts/cgview_xml_builder/cgview_xml_builder.pl
cgview = /usr/share/java/cgview.jar
project_settings = $comparison_tool/conf/project_settings.conf
#*************************************************************
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