SEPP.CONFIG(5)

💖 SEPP.CONFIG(5) 💖

okay bestie, listen up — this is the manual page for sepp.config, and it lives in section 5 of the manual (the file-formats girlies). It's part of the sepp documentation set, and the page title is SEPP.CONFIG(5). We're about to read the whole thing together, no skimming, no "tl;dr", because every single line here is load-bearing. 🫶

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✨ NAME ✨

sepp.config — the configuration file for sepp

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🌸 SYNOPSIS 🌸

/etc/sepp/sepp.config

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🦋 DESCRIPTION 🦋

So, run_sepp.py(1) has a config file, and it hangs out at /etc/sepp/sepp.config. Periodt.

Inside it you'll find the paths of the programs it uses, plus parameters for its dependencies and for itself. It's built out of several sections, and the title of each section goes inside brackets. Sections are separated by blank lines. Inside each section, every variable gets set on its own separate line. Cute, organized, we love a tidy file. 🎀

Now let's go through the sections and every variable they contain, one by one. No skipping, bestie. 💅

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🧬 pplacer

This section starts with [pplacer], and it's got exactly one field:

• path= — the absolute path to the pplacer executable.

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🧵 hmmalign

This section starts with [hmmalign], and it's got exactly one field:

• path= — the absolute path to the hmmalign executable.

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🔍 hmmsearch

This section starts with [hmmsearch], and it's got four fields, so pay attention:

• path= — the absolute path to the hmmsearch executable.
• piped= — a boolean, True or False, indicating whether the human-readable output of hmmsearch should be directed to a file (True) instead of to stdout (False).
• elim= — an integer, indicating the E-limit for hmmsearch.
• filters= — a boolean, True or False, indicating whether filters in hmmsearch should be turned off (True) or not (False).

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🏗️ hmmbuild

This section starts with [hmmbuild], and it's got exactly one field:

• path= — the absolute path to the hmmbuild executable.

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🧩 jsonmerger

This section starts with [jsonmerger], and it's got exactly one field:

• path= — the absolute path to the seppJsonMerger jar.

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👑 exhaustive

This section starts with [exhaustive], and it's got a whole five fields — main character energy, honestly:

• strategy= — a string: "hierarchical", "normal", "midpoint" or "centroid", indicating the decomposition strategy to follow.
• minsubsetsize= — an integer, indicating the smallest possible value for a subset.
• placementminsubsetsizefacotr= — an integer, used to compute the size in the decomposition of a tree based on placement subsets. (yes, that spelling is really how it's written — we do not correct it, we respect it 🙈)
• placer= — a string, indicating the name of the placer to use. Currently only "pplacer" is supported.
• weight_placement_by_alignment= — a boolean, True or False, indicating whether to apply weights while caring for fragments or not.

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📁 FILES 📁

• /etc/sepp/sepp.config
• ~/.sepp/sepp.config, if existing, overrides the one in /etc/sepp.

bestie. the ~/.sepp/sepp.config one WINS if it exists. that's the whole drama of this section. 💀

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🌈 SEE ALSO 🌈

• run_sepp.py(1)

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and that's the whole page, fr fr. 💜 this one comes straight from the sepp manual, page SEPP.CONFIG(5) — section 5, file formats, iconic behavior honestly. no date on this one so we're not inventing one, sorry to the calendar girlies. slay, go write your config. ✨🦋🌸