update-sort-bed-slurm - manual page for update-sort-bed-slurm
2.4.39+dfsg1
update-sort-bed-slurm
- citation:
http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.39 authors: Alex Reynolds and Shane Neph
- $ update-sort-bed-slurm [ --slurm-memory <MB>
]
- [ --slurm-partition <SLURM partition> ]
- [ --slurm-workdir <working directory> ] [
--slurm-output <SLURM output directory> ] [
--slurm-error <SLURM error directory> ] [
--bedextract-path <path to bedextract> ] [
--sort-bed-path <path to sort-bed> ] [ --debug ]
--input-original <old-bed-file> --input-backup
<renamed-old-bed-file> --output-temp
<intermediate-new-bed-file> --output-final
<new-bed-file>
- 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".
- When migration is finished, "--input-backup" specifies the new
name of the original input.
- As migration progresses, intermediate results are written to
"--output-temp" and then written to "--output-final"
upon completion.
- 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.
- 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 /tmp may fail, as the /tmp path is almost
certainly unique to a node; it is necesssary to use a path shared among
all nodes.
- 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.
- 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.
The full documentation for update-sort-bed-slurm is
maintained as a Texinfo manual. If the info and
update-sort-bed-slurm programs are properly installed at your site,
the command
- info update-sort-bed-slurm
should give you access to the complete manual.