update-sort-bed-migrate-candidates - manual page for
update-sort-bed-migrate-candidates 2.4.39+dfsg1
update-sort-bed-migrate-candidates
- citation:
http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.39 authors: Alex Reynolds and Shane Neph
- $ update-sort-bed-migrate-candidates [ --dry-run ] [
--debug ]
- [ --write-list |
- --resort-immediately | --resort-in-parallel-via-slurm
- [ --slurm-memory <MB> ]
- [ --slurm-partition <SLURM partition> ] [
--slurm-workdir <working directory> ] [ --slurm-output
<SLURM output directory> ] [ --slurm-error <SLURM error
directory> ]
- ]
- [ --bedops-root-dir <bedops directory> ] [
--bedextract-path <path> ] [ --sort-bed-path
<path> ] [ --unstarch-path <path> ] [
--starch-path <path> ] [ --starchcat-path <path>
] [ --update-sort-bed-slurm-path <path> ] [
--update-sort-bed-starch-slurm-path <path> ]
--parent-dir <parent directory> [
--non-recursive-search ]
- 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.
- 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.
- If the "--non-recursive-search" option is added, this utility
will only search within the specified parent directory, and go no
deeper.
- This utility offers one of three (exclusive) actions for migration:
- 1. Using "--write-list", files that require re-sorting can have
their paths
- written to standard output, which can be written to a file to be processed
later on, as desired.
- 2. Using "--resort-immediately", qualifying files can be
resorted immediately
- after all candidates are found, through a local, serial application of
'sort-bed'.
- 3. Using "--resort-in-parallel-via-slurm", candidate files can
be migrated by
- applying the 'update-sort-bed-slurm' script to resort in parallel on a
computational cluster managed with a SLURM job scheduler.
- Note that one of these three options must be chosen, to perform the stated
action, and only one option can be selected.
- 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.
- 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:
- 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.
---
- Suggestions:
- 1. Add the "--dry-run" option to
"--resort-immediately" or the
- "--resort-in-parallel-via-slurm" options to see the behavior
before any filesystem actions are performed. Remove "--dry-run"
to perform the specified work.
- 2. If you use the resort-via-SLURM option, consider using
"--slurm-memory",
- "--slurm-partition", "--slurm-workdir",
"--slurm-output", and "--slurm-error" options to match
the setup of your particular cluster environment and inputs.
- 3. Add "--debug" option to log debug statements to get more
detail about
- internal operation of update process.
The full documentation for
update-sort-bed-migrate-candidates is maintained as a Texinfo manual.
If the info and update-sort-bed-migrate-candidates programs
are properly installed at your site, the command
- info update-sort-bed-migrate-candidates
should give you access to the complete manual.