UPDATE-SORT-BED-SLURM(1)

✨ UPDATE-SORT-BED-SLURM ✨

okay bestie, gather round 💖 this is the manual page for update-sort-bed-slurm, and it comes to you straight from version 2.4.42+dfsg. it's a whole little utility, it's lowkey iconic, and it has opinions about your BED files. let's get into it 🦋

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🌸 NAME 🌸

update-sort-bed-slurm — the manual page for update-sort-bed-slurm 2.4.42+dfsg. that's it, that's the name, she's self-titled 💅

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🎀 DESCRIPTION 🎀

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

version: 2.4.42

authors: Alex Reynolds and Shane Neph

okay so here's the vibe. the whole invocation looks like this:

$ 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>

so what does she do, you ask? 🧚 the update-sort-bed-slurm utility applies an updated sort order on BED files that were sorted per pre-v2.4.20 sort-bed. she does this using a SLURM job scheduler to coordinate resorting each chromosome in --input-original per post-v2.4.20 sort-bed, and then she writes the result out to --output-final. slay ✨

when the migration is finished, --input-backup specifies the new name of the original input. no cap, that's the rename step 💖

as migration progresses, intermediate results are written to --output-temp and then written to --output-final upon completion. so it's a little journey, and you get to watch it happen 🌈

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. not me warning you about this, it's literally in the docs 🔥

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 necessary to use a path shared among all nodes. this is the main character energy of gotchas, bestie, do not skip it 🙈

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. she's specific like that 💅

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 pre-v2.4.20 order, or which do not follow exact specification — all of which can lead a per-chromosome resort task to fail. 💀 silent failure is the villain of this whole story, so please read that twice.

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👑 the options, in full

• --slurm-memory <MB> — how much memory each sort task gets, in MB. leave it alone and every task gets 8 GB. bigger input? bigger number, periodt.
• --slurm-partition <SLURM partition> — which SLURM partition the work gets assigned to. default vibe is queue0.
• --slurm-workdir <working directory> — the working directory for the SLURM side of things.
• --slurm-output <SLURM output directory> — where SLURM should drop its output.
• --slurm-error <SLURM error directory> — where SLURM should drop its errors. (yes, you want this one, fr fr.)
• --bedextract-path <path to bedextract> — the path to bedextract.
• --sort-bed-path <path to sort-bed> — the path to sort-bed.
• --debug — turns on debug mode. the little spyglass of the whole operation 🔍
• --input-original <old-bed-file> — your old BED file, the one sorted the pre-v2.4.20 way. this is the one getting resorted, chromosome by chromosome.
• --input-backup <renamed-old-bed-file> — the new name the original input gets once migration is finished.
• --output-temp <intermediate-new-bed-file> — the intermediate new BED file, where progress lands while things are still cooking.
• --output-final <new-bed-file> — the final new BED file, written once everything is complete. the glow-up destination 🦋

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💜 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, this command:

info update-sort-bed-slurm

should give you access to the complete manual. go get that lore, bestie 📖✨

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and that's the whole page, bestie 🫶 this was update-sort-bed-slurm 2.4.42+dfsg, dated August 2025 — and it was so nice to read for you. now go allocate more than 8 GB if you need to, and please use a shared path 💖🎀🌸