Low Level Global Configuration

The [module_list] section contains definitions of the MODULE_PATH and MODULES variables. The MODULE_PATH is a space delimited list of directory names in which to search for the pregap4 modules (*.p4m files). The MODULES variable is the default list of modules to list in the configuration window. The order of modules in this list determines the order that they will be executed in. The default [module_list] section is as follows:

[module_list]
set MODULE_PATH "$env(STADLIB)/pregap4/modules ."
set MODULES {
    phred
    atqa
    convert_trace
    eba
    compress_trace
    init_exp
    augment_exp
    quality_clip
    trace_clip
    sequence_vector_clip
    cross_match_svec
    cloning_vector_clip
    screen_vector
    screen_seq
    blast
    interactive_clip
    repeat_masker
    tag_repeats
    trace_diff
    gap4_assemble
    cap2_assemble
    cap3_assemble
    fakii_assemble
    phrap_assemble
    enter_assembly
    email
}

The [global_variables] section defines the values for each of the Experiment File line types. These are currently primarily used by the Augment Experiment Files module, but may also be used by the vector clipping and mutation detection modules. The default [global_variables] section is blank.

As an example, the following section defines the sequencing vector file for each sequence to be m13mp18.vector with 6249 and 41 as the cut site and primer site. Each sequence has a primer type of 1 (forward universal primer) and the template name is derived from the sequence name by taking the segment of the string preceding the full stop.

[global_variables]
set SF m13mp18.vector
set SC 6249
set SP 41
set PR 1
proc TN_com {} { global lines; return [lindex [split $lines(ID) .] 0] }