Provided by: bedops_2.4.41+dfsg-1_amd64 bug

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+dfJuly 2022       UPDATE-SORT-BED-MIGRATE-CANDIDATES(1)