NAME

       update-sort-bed-migrate-candidates - manual page for update-sort-bed-migrate-candidates 2.4.37+dfsg

DESCRIPTION

       update-sort-bed-migrate-candidates

              citation:  http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract  version:   2.4.37
              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.