TIPP.CONFIG(5)

📦 version 1.0, in ubuntu jammy

🎀 TIPP.CONFIG(5) — the tipp.config girlies' guide 🎀

okay so bestie, you're here for the tipp.config manual page (that's the manual name, section 5, we're doing config files today 💅) and honestly? it's giving "short and sweet and also extremely load-bearing." let's get into it 🦋

✨ NAME ✨

tipp.config — the configuration for tipp. that's it, that's the whole vibe. periodt. 💖

✨ SYNOPSIS ✨

/etc/tipp/tipp.config

✨ DESCRIPTION ✨

so the config file for run_tipp.py(1) lives at /etc/tipp/tipp.config. it's where you tell tipp where all its little program besties are, plus the parameters for its dependencies and for itself. it's literally the group chat settings page of the whole operation 🫶

the file is made of several sections, and each section's title gets put inside brackets — like [pplacer] — because brackets are the moment. sections are separated by blank lines. inside each section, every variable gets set on its own separate line. no cramming, we don't do that here ✨

and now, bestie, we list the sections and the variables they contain. buckle up 🌸

🌈 pplacer

this section begins with [pplacer], and it has the following field:

  • path= — the absolute path to the pplacer executable. absolute. like, full path energy. no shortcuts 👑

🌈 hmmalign

this section begins with [hmmalign], and it has the following field:

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

🌈 hmmsearch

this section begins with [hmmsearch], and it has the following fields:

  • 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 stdout (False). pick your lane, output 🎀
  • 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). True means filters OFF, False means filters stay on — yes, that's the way it's written, don't @ me, I just report the lore 💀

🌈 hmmbuild

this section begins with [hmmbuild], and it has the following field:

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

🌈 jsonmerger

this section begins with [jsonmerger], and it has the following field:

  • path= — the absolute path to the tippJsonMerger jar. yes, a jar. java girlies rise 🫙✨

🌈 exhaustive

this section begins with [exhaustive], and it has the following fields:

  • strategy= — a string, either "hierarchical", "normal", "midpoint" or "centroid", indicating the decomposition strategy to follow. choose your fighter 🌈
  • minsubsetsize= — an integer, indicating the smallest possible value for a subset. no subset smaller than this, bestie, we have standards 💅
  • placementminsubsetsizefacotr= — an integer, used to compute the size in the decomposition of a tree based on placement subsets. (yes the name has a typo in it — facotr — and yes you must spell it exactly like that, I don't make the rules, I just simp for them 😭)
  • placer= — a string, indicating the name of the placer to use. currently only "pplacer" is supported. one placer to rule them all 👑
  • weight_placement_by_alignment= — a boolean True or False, indicating whether to apply weights while caring for fragments or not. 🧚

🌈 blast

this section begins with [blast], and it has the following field:

  • path= — the absolute path to the blastn executable. 🔥

🌈 reference

this section begins with [reference], and it has the following field:

  • path= — the absolute path to the reference dataset. here's the cute part: this dataset may be downloaded, placed into a directory, and then the current field in the configuration file tipp.config can be edited so that it points to the location of the dataset. so like, download it, park it somewhere, then point at it. easy 🍓

🌈 tipp

this section begins with [tipp], and it has the following field:

  • pushdown= — a boolean set to true, although it is not used by tipp at the moment. it's just there. chilling. main character energy with zero lines 🙈

✨ FILES ✨

  • /etc/tipp/tipp.config
  • ~/.tipp/tipp.config, if existing, overrides the one in /etc/tipp. so your home one is the boss if it shows up — lowkey iconic ✨

✨ SEE ALSO ✨

run_tipp.py(1), sepp.config(5)

go read those too bestie, iykyk 📚💖

and that's the whole page, no cap 🫶 this was TIPP.CONFIG(5) from the tipp source — thanks for scrolling all the way down, you ate 💅✨

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