UPDATE-SORT-BED-STARCH-SLURM(1)

📦
version 2.4.42 · 5 versions
, in ubuntu resolute, ubuntu stonking

✨ NAME ✨

okay so bestie, say hi to update-sort-bed-starch-slurm 💖 — it's a manual page for the thing itself, update-sort-bed-starch-slurm version 2.4.42+dfsg. yes the whole name, she's long, she's iconic, she contains multitudes. 👑

🌸 DESCRIPTION 🌸

so. update-sort-bed-starch-slurm — no cap, that's the whole vibe. it's giving:

and like, here's how you actually run her:

$ 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 flags, one by one (do not lose a single one, i'm serious)

  • --slurm-memory <MB> — how much memory each SLURM sort task gets. defaults to 8 GB if you don't say anything.
  • --slurm-partition <SLURM partition> — which cluster partition the work gets launched on. defaults to the "queue0" partition unless you set this.
  • --slurm-workdir <working directory> — the working directory for the SLURM side of things.
  • --slurm-output <SLURM output directory> — where SLURM drops its output.
  • --slurm-error <SLURM error directory> — where SLURM drops its errors. 🫶
  • --bedextract-path <path to bedextract> — path to the bedextract binary.
  • --sort-bed-path <path to sort-bed> — path to the sort-bed binary.
  • --unstarch-path <path to unstarch> — path to the unstarch binary.
  • --starch-path <path to starch> — path to the starch binary.
  • --starchcat-path <path to starchcat> — path to the starchcat binary.
  • --debug — debug mode, turn it on.
  • --input-original <old-bed-file> — your original, pre-v2.4.20-sorted Starch input file. required, fr fr.
  • --input-backup <renamed-old-bed-file> — what the original input file gets renamed to when migration finishes. required.
  • --output-temp <intermediate-new-bed-file> — the intermediate new BED file that gets written as migration progresses. required.
  • --output-final <new-bed-file> — the final new BED file that the result lands in. required.

okay so what does she do?? the update-sort-bed-starch-slurm utility applies an updated sort order on Starch files that were sorted per pre-v2.4.20 sort-bed, and she uses a SLURM job scheduler to coordinate resorting each chromosome in "--input-original" per post-v2.4.20 sort-bed, then writes the result to a Starch file at "--output-final". slay. 💅

when migration is finished, "--input-backup" specifies the new name of the original input file. that's the glow-up, the rebrand, the new identity. ✨

as migration progresses, intermediate results are written to "--output-temp" and then written to "--output-final" upon completion. so you can literally watch her cook. 🔥

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. so if your input is bigger than 8 GB, bestie, you WILL need to allocate more memory. don't play yourself. 😭

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. (and yes, "necesssary" is spelled exactly like that in the original, i'm keeping it, it's part of her lore. 🙈)
note that this utility will not work on entirely unsorted BED files — only on files with a sort order from pre-v2.4.20 sort-bed, where there are ties on the first three columns. so it's a very specific girl in a very specific era. 🦋

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. 💀 yeah. silent failure. the worst kind. be careful out there.

🌈 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. go read it, bestie, she's thorough. 📖💜

and that's the whole page!! 💖 this one's from update-sort-bed-starch-slurm 2... (the version string the footer shows, she's mysterious like that ✨), dated August 2025, and the page itself is UPDATE-SORT-BED-STARCH-SLURM(1) in the User Commands section. okay bye ily, go resort responsibly 🫶🎀

📦 where this page comes from