.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH BUILD_BLAST_ATLAS_ALL_VS_ALL "1" "August 2018" "build_blast_atlas_all_vs_all 20170919" "User Commands"
.SH NAME
build_blast_atlas_all_vs_all \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
.SH DESCRIPTION
.SS "USAGE:"
.IP
build_blast_atlas_all_vs_all \fB\-p\fR DIR [Options]
.SS "DESCRIPTION:"
.IP
This script generates several CCT projects automatically, and then it
combines the results into a single montage map. The montage consists
of a separate map for each sequence of interest. This allows each sequence
in a group of sequences to be visualized as the reference sequence.
.IP
This command is used to first create a blast atlas all vs all project
directory and then again to generate the montage. After the project has
been created, place the genomes to compare in the comparison_genomes
directory.
.IP
[Optional] Make changes to the project_settings_multi.conf file to
configure how the maps will be drawn. Add additional GFF files to the
features and analysis directories.
.IP
Draw maps by running this command again with the '\-p' option pointing to the
project directory.
.SS "REQUIRED ARGUMENTS:"
.HP
\fB\-p\fR, \fB\-\-project\fR DIR
.IP
If no project exists yet, creates a new project directory. Otherwise,
initiates map creation for the project.
.SS "OPTIONAL ARGUMENTS:"
.HP
\fB\-m\fR, \fB\-\-memory\fR STRING
.IP
Memory value for Java's \fB\-Xmx\fR option (Default: 1500m).
.HP
\fB\-c\fR, \fB\-\-custom\fR STRING
.IP
Custom settings for map creation.
.HP
\fB\-b\fR, \fB\-\-max_blast_comparisons\fR INTEGER
.IP
Maximum number of comparison genomes to display (Default: 100).
.HP
\fB\-z\fR, \fB\-\-map_size\fR STRING
.IP
Size of custom maps to create. For quickly regenerating new map sizes,
use this option with the \fB\-\-start_at_xml\fR option. Possible sizes include
small/medium/large/x\-large or a combination separated by commas (e.g.
small,large). The size(s) provided will override the size(s) in the
configuration files.
.HP
\fB\-x\fR, \fB\-\-start_at_xml\fR
.IP
Jump to XML generation. Skips performing blast, which can
speed map generation if blast has already been done. This option is for
creating new maps after making changes to the .conf files or if creating
new map sizes (see \fB\-\-map_size\fR). Note that any changes in the .conf files
related to blast will be ignored. This option will be ignored if the
\fB\-\-start_at_map\fR or \fB\-\-start_at_montage\fR option is also provided.
.HP
\fB\-r\fR, \fB\-\-start_at_map\fR
.IP
Start at map generation. Skips performing blast and
generating XML. Useful if manual changes to the XML files have
been made. This option will be ignored if the \fB\-\-start_at_montage\fR
option is also provided.
.HP
\fB\-g\fR, \fB\-\-start_at_montage\fR
.IP
Start at montage generation. Skips creating the individual maps.
Useful if changing how many columns the montage should have.
.HP
\fB\-y\fR, \fB\-\-columns\fR INTEGER
.IP
The number of columns to use in the montage image (Default: 4). If the
maps have already been drawn once, it is best to use this option with the
\fB\-\-start_at_montage\fR option.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Show this message.
.SS "NOTES:"
.IP
This script will likely not work if there are spaces in the path to the
project directory because the NCBI tool 'formatdb' cannot handle such
paths.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.