.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH UPDATE-SORT-BED-SLURM "1" "July 2022" "update-sort-bed-slurm 2.4.41+dfsg" "User Commands"
.SH NAME
update-sort-bed-slurm \- manual page for update-sort-bed-slurm 2.4.41+dfsg
.SH DESCRIPTION
update\-sort\-bed\-slurm
.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-slurm [ --slurm-memory <MB> ]\fR
.TP
[ \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> ]
[ \fB\-\-bedextract\-path\fR <path to bedextract> ]
[ \fB\-\-sort\-bed\-path\fR <path to sort\-bed> ]
[ \fB\-\-debug\fR ]
\fB\-\-input\-original\fR <old\-bed\-file>
\fB\-\-input\-backup\fR <renamed\-old\-bed\-file>
\fB\-\-output\-temp\fR <intermediate\-new\-bed\-file>
\fB\-\-output\-final\fR <new\-bed\-file>
.IP
The "update\-sort\-bed\-slurm" utility applies an updated sort order on BED
files sorted per pre\-v2.4.20 sort\-bed, using a SLURM job scheduler to
coordinate resorting each chromosome in "\-\-input\-original" per post\-v2.4.20
sort\-bed and writing the result to "\-\-output\-final".
.IP
When migration is finished, "\-\-input\-backup" specifies the new name of the
original input.
.IP
As migration progresses, intermediate results are written to "\-\-output\-temp"
and then written to "\-\-output\-final" upon completion.
.IP
Each sort task is given 8 GB of memory and is assigned to the "queue0"
partition, unless the "\-\-slurm\-memory" and "\-\-slurm\-partition" options are
set. If your input is larger than 8 GB, you will need to allocate more
memory.
.IP
Because this launches all work on the specified cluster partition, the paths
specified by "\-\-input\-original", "\-\-input\-backup", "\-\-output\-final", and
"\-\-output\-temp" must be accessible to all computational nodes. For example,
using \fI\,/tmp\/\fP may fail, as the \fI\,/tmp\/\fP path is almost certainly unique to a node;
it is necesssary to use a path shared among all nodes.
.IP
Note that this utility will not work on entirely unsorted BED files, but only
on files with a sort order from pre\-v2.4.20 sort\-bed, where there are ties on
the first three columns.
.IP
In fact, until further refinements are made, this convenience utility could
fail silently on inputs which are not BED, or which are not sorted per prev2.4.20 order, or which do not follow exact specification, all of which can
lead a per\-chromosome resort task to fail.
.SH "SEE ALSO"
The full documentation for
.B update-sort-bed-slurm
is maintained as a Texinfo manual.  If the
.B info
and
.B update-sort-bed-slurm
programs are properly installed at your site, the command
.IP
.B info update-sort-bed-slurm
.PP
should give you access to the complete manual.