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] }