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.

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