update-sort-bed-migrate-candidates1

Overview

update-sort-bed-migrate-candidates

citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract version: 2.4.41 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.