.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH UPDATE-SORT-BED-MIGRATE-CANDIDATES "1" "July 2022" "update-sort-bed-migrate-candidates 2.4.41+dfsg" "User Commands"
.SH NAME
update-sort-bed-migrate-candidates \- manual page for update-sort-bed-migrate-candidates 2.4.41+dfsg
.SH DESCRIPTION
update\-sort\-bed\-migrate\-candidates
.IP
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version:  2.4.41
authors:  Alex Reynolds and Shane Neph
.IP
\f(CW$ update-sort-bed-migrate-candidates [ --dry-run ] [ --debug ]\fR
.TP
[ \fB\-\-write\-list\fR |
\fB\-\-resort\-immediately\fR |
\fB\-\-resort\-in\-parallel\-via\-slurm\fR
.TP
[ \fB\-\-slurm\-memory\fR <MB> ]
[ \fB\-\-slurm\-partition\fR <SLURM partition> ]
[ \fB\-\-slurm\-workdir\fR <working directory> ]
[ \fB\-\-slurm\-output\fR <SLURM output directory> ]
[ \fB\-\-slurm\-error\fR <SLURM error directory> ]
.TP
]
[ \fB\-\-bedops\-root\-dir\fR <bedops directory> ]
[ \fB\-\-bedextract\-path\fR <path> ]
[ \fB\-\-sort\-bed\-path\fR <path> ]
[ \fB\-\-unstarch\-path\fR <path> ]
[ \fB\-\-starch\-path\fR <path> ]
[ \fB\-\-starchcat\-path\fR <path> ]
[ \fB\-\-update\-sort\-bed\-slurm\-path\fR <path> ]
[ \fB\-\-update\-sort\-bed\-starch\-slurm\-path\fR <path> ]
\fB\-\-parent\-dir\fR <parent directory>
[ \fB\-\-non\-recursive\-search\fR ]
.IP
The "update\-sort\-bed\-migrate\-candidates" utility recursively locates BED and
Starch files in the specified parent directory and tests if they require
re\-sorting to conform to the updated, post\-v2.4.20 "sort\-bed" order.
.IP
Files with the extensions starch, bstarch, gstarch, bed, or bed[g|G]raph in
the parent directory are tested. Files without these extensions are ignored.
.IP
If the "\-\-non\-recursive\-search" option is added, this utility will only search
within the specified parent directory, and go no deeper.
.IP
This utility offers one of three (exclusive) actions for migration:
.IP
1. Using "\-\-write\-list", files that require re\-sorting can have their paths
.IP
written to standard output, which can be written to a file to be processed
later on, as desired.
.IP
2. Using "\-\-resort\-immediately", qualifying files can be resorted immediately
.IP
after all candidates are found, through a local, serial application of
\&'sort\-bed'.
.IP
3. Using "\-\-resort\-in\-parallel\-via\-slurm", candidate files can be migrated by
.IP
applying the 'update\-sort\-bed\-slurm' script to resort in parallel on a
computational cluster managed with a SLURM job scheduler.
.IP
Note that one of these three options must be chosen, to perform the
stated action, and only one option can be selected.
.IP
When using "\-\-resort\-immediately" or "\-\-resort\-in\-parallel\-via\-slurm", the
resorted files will have the name of the original BED or Starch file. The
original files will have their old name, with the ".backup" extension.
.IP
Use the "\-\-bedops\-root\-dir" option to specify the directory containing the
BEDOPS toolkit binaries to be used for migration. You can provide more specific
paths to individual binaries, using the following options:
.IP
Add the "\-\-bedextract\-path", "\-\-sort\-bed\-path", "\-\-unstarch\-path",
"\-\-starch\-path", "\-\-starchcat\-path", "\-\-update\-sort\-bed\-slurm", and/or
"\-\-update\-sort\-bed\-starch\-slurm" options to specify custom paths to versions
of these tools, if desired. These values will be passed along to downstream
helper scripts that use them.
.HP
\fB\-\-\-\fR
.IP
Suggestions:
.IP
1. Add the "\-\-dry\-run" option to "\-\-resort\-immediately" or the
.IP
"\-\-resort\-in\-parallel\-via\-slurm" options to see the behavior before any
filesystem actions are performed. Remove "\-\-dry\-run" to perform the
specified work.
.IP
2. If you use the resort\-via\-SLURM option, consider using "\-\-slurm\-memory",
.IP
"\-\-slurm\-partition", "\-\-slurm\-workdir", "\-\-slurm\-output", and
"\-\-slurm\-error" options to match the setup of your particular cluster
environment and inputs.
.IP
3. Add "\-\-debug" option to log debug statements to get more detail about
.IP
internal operation of update process.
.SH "SEE ALSO"
The full documentation for
.B update-sort-bed-migrate-candidates
is maintained as a Texinfo manual.  If the
.B info
and
.B update-sort-bed-migrate-candidates
programs are properly installed at your site, the command
.IP
.B info update-sort-bed-migrate-candidates
.PP
should give you access to the complete manual.