/usr/share/staden/etc/cap2rc 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 | load_package %L/cap2 {} cap2 0
set_menu gap_menu
add_menu Assembly 1 2 left
set fs ""
catch {set fs [open "|cap2_s" r]}
if {$fs == ""} {
add_cascade {Assembly.CAP2 Assembly} 0 0
} else {
catch {close $fs}
add_cascade {Assembly.CAP2 Assembly} 12 22
}
add_command {Assembly.CAP2 Assembly.Perform CAP2 assembly} \
12 22 {HuangAssembly \$io 1}
add_command {Assembly.CAP2 Assembly.Import CAP2 assembly data} \
12 22 {HuangImport \$io}
add_command {Assembly.CAP2 Assembly.Perform and import CAP2 assembly} \
12 22 {HuangAssembly \$io 2}
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_def HUANG_ASSEMBLY1.WIN .cap2_perform_assembly
set_def HUANG_ASSEMBLY2.WIN .cap2_import_assembly
set_def HUANG_ASSEMBLY3.WIN .cap2_perform_import_assembly
set_def HUANG_ASSEMBLY.INFILE $defs_f_or_l_in
set_def HUANG_ASSEMBLY.INFILE.WHICH.NAME "Input readings from"
set_def HUANG_ASSEMBLY.DEST.NAME "Destination directory"
set_def HUANG_ASSEMBLY.DEST.VALUE "assemble"
set_def HUANG_ASSEMBLY.FORMAT.NAME "Input reading format"
set_def HUANG_ASSEMBLY.FORMAT.VALUE 1
set_def HUANG_ASSEMBLY.FORMAT.BUTTON.1 "experiment"
set_def HUANG_ASSEMBLY.FORMAT.BUTTON.2 "fasta"
set_def HUANG_ASSEMBLY.REPEAT.NAME "Find repeats/chimerics"
set_def HUANG_ASSEMBLY.REPEAT.VALUE 1
set_def HUANG_ASSEMBLY.OUTFILE $defs_f_or_l_out
set_def HUANG_ASSEMBLY.OUTFILE.WHICH.NAME "Save failures to"
set_def HUANG_ASSEMBLY.INDIR.NAME "Directory containing assembled readings"
set_def HUANG_ASSEMBLY.FOFN "outfile"
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