NAME

       update-sort-bed-slurm - manual page for update-sort-bed-slurm 2.4.41+dfsg

DESCRIPTION

       update-sort-bed-slurm

              citation:      http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
              version:  2.4.41 authors:  Alex Reynolds and Shane Neph

              $ update-sort-bed-slurm [ --slurm-memory <MB> ]

       [ --slurm-partition <SLURM partition> ]
              [ --slurm-workdir <working directory> ] [ --slurm-output <SLURM output directory> ]
              [  --slurm-error <SLURM error directory> ] [ --bedextract-path <path to bedextract>
              ]  [  --sort-bed-path  <path  to  sort-bed>  ]   [   --debug   ]   --input-original
              <old-bed-file>       --input-backup       <renamed-old-bed-file>      --output-temp
              <intermediate-new-bed-file> --output-final <new-bed-file>

              The "update-sort-bed-slurm" utility applies an updated  sort  order  on  BED  files
              sorted  per  pre-v2.4.20  sort-bed,  using  a  SLURM  job  scheduler  to coordinate
              resorting each chromosome  in  "--input-original"  per  post-v2.4.20  sort-bed  and
              writing the result to "--output-final".

              When migration is finished, "--input-backup" specifies the new name of the original
              input.

              As migration progresses, intermediate results are written  to  "--output-temp"  and
              then written to "--output-final" upon completion.

              Each  sort  task is given 8 GB of memory and is assigned to the "queue0" partition,
              unless the "--slurm-memory" and "--slurm-partition" options are set. If your  input
              is larger than 8 GB, you will need to allocate more memory.

              Because  this  launches  all  work  on  the  specified cluster partition, the paths
              specified   by   "--input-original",   "--input-backup",   "--output-final",    and
              "--output-temp"  must  be accessible to all computational nodes. For example, using
              /tmp may fail, as the /tmp path is  almost  certainly  unique  to  a  node;  it  is
              necesssary to use a path shared among all nodes.

              Note  that  this  utility will not work on entirely unsorted BED files, but only on
              files with a sort order from pre-v2.4.20 sort-bed, where  there  are  ties  on  the
              first three columns.

              In  fact,  until  further refinements are made, this convenience utility could fail
              silently on inputs which are not BED, or which are not sorted per prev2.4.20 order,
              or  which do not follow exact specification, all of which can lead a per-chromosome
              resort task to fail.

SEE ALSO

       The full documentation for update-sort-bed-slurm is maintained as a  Texinfo  manual.   If
       the  info  and  update-sort-bed-slurm  programs  are  properly installed at your site, the
       command

              info update-sort-bed-slurm

       should give you access to the complete manual.