/usr/share/staden/etc/fak2rc is in staden-common 2.0.0+b11-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 | load_package %L/fak2 {} fak2 0
set_menu gap_menu
add_menu Assembly 1 2 left
set fs ""
catch {set fs [open "|write_exp_file" r]}
if {$fs == ""} {
add_cascade {Assembly.Fak2 Assembly} 0 0
} else {
catch {close $fs}
add_cascade {Assembly.Fak2 Assembly} 12 22
}
add_command {Assembly.Fak2 Assembly.Perform FAKII assembly} \
12 22 {Fak2Assembly \$io}
add_command {Assembly.Fak2 Assembly.Import FAKII assembly data} \
12 22 {Fak2Import \$io}
add_command {Assembly.Fak2 Assembly.Perform and import FAKII assembly} \
12 22 {Fak2AssemblyImport \$io}
set_defx defs_f_or_l_in WHICH.NAME "Input from"
set_defx defs_f_or_l_in WHICH.BUTTONS {list file}
set_defx defs_f_or_l_in WHICH.VALUE 2
set_defx defs_f_or_l_in NAME.NAME "List or file name"
set_defx defs_f_or_l_in NAME.BROWSE "Browse"
set_defx defs_f_or_l_in NAME.VALUE ""
set_defx defs_f_or_l_out WHICH.NAME "Output to"
set_defx defs_f_or_l_out WHICH.BUTTONS {list file}
set_defx defs_f_or_l_out WHICH.VALUE 2
set_defx defs_f_or_l_out NAME.NAME "List or file name"
set_defx defs_f_or_l_out NAME.BROWSE "Browse"
set_defx defs_f_or_l_out NAME.VALUE ""
set_defx defs_c_in WHICH.NAME "Input contigs from"
set_defx defs_c_in WHICH.BUTTONS {list file {{all contigs}} single}
set_defx defs_c_in WHICH.VALUE 3
set_defx defs_c_in NAME.NAME "List or file name"
set_defx defs_c_in NAME.BROWSE "Browse"
set_defx defs_c_in NAME.VALUE ""
set_def BINARIES $env(STADENROOT)/bin
set_def FAK2_ASSEMBLY1.WIN .fakii_perform_assembly
set_def FAK2_ASSEMBLY2.WIN .fakii_import_assembly
set_def FAK2_ASSEMBLY3.WIN .fakii_perform_import_assembly
set_def FAK2_ASSEMBLY.INFILE $defs_f_or_l_in
set_def FAK2_ASSEMBLY.INFILE.WHICH.NAME "Input readings from"
set_def FAK2_ASSEMBLY.FORMAT.NAME "Input reading format"
set_def FAK2_ASSEMBLY.FORMAT.VALUE 1
set_def FAK2_ASSEMBLY.FORMAT.BUTTON.1 "experiment"
set_def FAK2_ASSEMBLY.FORMAT.BUTTON.2 "fasta"
set_def FAK2_ASSEMBLY.GRAPH.E_LMT.NAME "Error limit"
set_def FAK2_ASSEMBLY.GRAPH.E_LMT.VALUE 0.099
set_def FAK2_ASSEMBLY.GRAPH.E_LMT.MIN 0
set_def FAK2_ASSEMBLY.GRAPH.E_LMT.MAX 0.25
set_def FAK2_ASSEMBLY.GRAPH.D_LMT.NAME "Distribution limit"
set_def FAK2_ASSEMBLY.GRAPH.D_LMT.VALUE 0.0001
set_def FAK2_ASSEMBLY.GRAPH.D_LMT.MIN 0.0
set_def FAK2_ASSEMBLY.GRAPH.D_LMT.MAX 0.1
set_def FAK2_ASSEMBLY.GRAPH.O_THR.NAME "Overlap threshold"
set_def FAK2_ASSEMBLY.GRAPH.O_THR.VALUE 10.0
set_def FAK2_ASSEMBLY.GRAPH.CONS.NAME "Use constraint file"
set_def FAK2_ASSEMBLY.GRAPH.CONS.VALUE 0
set_def FAK2_ASSEMBLY.ASSEM.A_NUM.NAME "Assembly number"
set_def FAK2_ASSEMBLY.ASSEM.A_NUM.VALUE 1
set_def FAK2_ASSEMBLY.ASSEM.CONS.NAME "File of constraints (optional)"
set_def FAK2_ASSEMBLY.ASSEM.DEST.NAME "Destination directory"
set_def FAK2_ASSEMBLY.ASSEM.DEST.VALUE "assemble"
set_def FAK2_ASSEMBLY.ASSEM.CONS.VALUE ""
set_def FAK2_ASSEMBLY.ASSEM.E_RATE.NAME "Error rate"
set_def FAK2_ASSEMBLY.ASSEM.E_RATE.VALUE 0.05
set_def FAK2_ASSEMBLY.ASSEM.O_THR.NAME "Overlap threshold"
set_def FAK2_ASSEMBLY.ASSEM.O_THR.VALUE 20.0
set_def FAK2_ASSEMBLY.ASSEM.D_THR.NAME "Distribution threshold"
set_def FAK2_ASSEMBLY.ASSEM.D_THR.VALUE 0.0001
set_def FAK2_ASSEMBLY.ASSEM.D_THR.MIN 0
set_def FAK2_ASSEMBLY.ASSEM.D_THR.MAX 0.1
set_def FAK2_ASSEMBLY.ASSEM.VIEW.BUTTON.1 "Show layout"
set_def FAK2_ASSEMBLY.ASSEM.VIEW.BUTTON.2 "Show multi-alignment"
set_def FAK2_ASSEMBLY.ASSEM.VIEW.NAME "Output"
set_def FAK2_ASSEMBLY.ASSEM.VIEW.VALUE 1
set_def FAK2_ASSEMBLY.OUTFILE $defs_f_or_l_out
set_def FAK2_ASSEMBLY.OUTFILE.WHICH.NAME "Save failures to"
set_def FAK2_ASSEMBLY.INDIR.NAME "Directory containing assembly"
set_def FAK2_ASSEMBLY.FOFN "outfile"
set_def FAK2_ASSEMBLY.BINARY "assem.bin"
set_def FAK2_ASSEMBLY.G_BINARY "graph.bin"
set_def FAK2_ASSEMBLY.CONSTRAINT_B "constraint.bin"
set_def FAK2_ASSEMBLY.CONSTRAINT_A "constraint.ascii"
set_def FAK2_ASSEMBLY.IMPORT.INFILE $defs_c_in
set_def FAK2_ASSEMBLY.IMPORT.FLAG.NAME "Use existing experiment files"
set_def FAK2_ASSEMBLY.IMPORT.FLAG.VALUE 1
set_def FAK2_ASSEMBLY.IMPORT.C_NUM.NAME "Contig number"
set_def FAK2_ASSEMBLY.IMPORT.C_NUM.VALUE 0
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