NAME

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

DESCRIPTION

       update-sort-bed-starch-slurm

              citation:  http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract  version:   2.4.41
              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.

update-sort-bed-starch-slurm 2.4.41+dfsg           April 2024                    UPDATE-SORT-BED-STARCH-SLURM(1)