NAME

       update-sort-bed-migrate-candidates - manual page for update-sort-bed-migrate-candidates 2.4.41+dfsg

DESCRIPTION

       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.

SEE ALSO

       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.

update-sort-bed-migrate-candidates 2.4.41+dfsg     April 2024              UPDATE-SORT-BED-MIGRATE-CANDIDATES(1)