NAME

       update-sort-bed-starch-slurm - manual page for update-sort-bed-starch-slurm 2.4.40+dfsg

DESCRIPTION

       update-sort-bed-starch-slurm

              citation:      http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
              version:  2.4.40 authors:  Alex Reynolds and Shane Neph

              $ update-sort-bed-starch-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> ] [ --unstarch-path <path to unstarch>  ]  [
              --starch-path <path to starch> ] [ --starchcat-path <path to starchcat> ] [ --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-starch-slurm' utility applies an updated sort order on Starch
              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 a Starch file at "--output-final".

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

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

              info update-sort-bed-starch-slurm

       should give you access to the complete manual.