LogolMultiExec(1)

okay bestie, this is the LogolMultiExec(1) manual, filed under USER COMMANDS 🧚 let's get into it ✨

✨ NAME ✨

okay so LogolMultiExec is the program that parses a logol grammar and searches for patterns in a sequence 💅 it lets you run the LogolExec program on multi fasta input, and then it dispatches all the work either to a DRMAA compliant grid or to multi-cpu servers 🖥️ literally so main character 🔥

🌸 SYNOPSIS 🌸

LogolMultiExec [-h]

🔧 INSTALLATION 🔧

bestie, this needs the drmaa library 🫶 the default is to use the SGE library. if you're using a different one, you gotta update the symbolic link at /usr/share/logol/lib/drmaa.jar so it points to the right library 🔗

also, LD_LIBRARY_PATH must be updated in /sur/share/logol/LogolMultiExec.sh 🙈

heads up: the page spells that path as /sur/, which looks like a typo for /usr/. i'm keeping it exactly as written so nothing gets lost in translation 💀

⚙️ CONFIGURATION ⚙️

LogolMultiExec and LogolExec share the same configuration file 🫶 check the LogolExec man page for more info 📖

a stray .PP also snuck into this section 🙈

👑 OPTIONS 👑

the minimum arguments are -m for a logol model or -g for a logol grammar, plus -s for the input sequence 💖

🎀 MAIN OPTIONS 🎀

• -h — shows you the list of commands 📜
• -v — get the version 🦋
• -conf — specify the configuration file ⚙️
• -s — the sequence file to analyse 🧬
• -g — the grammar file to analyse 📝
• -m — the model file to analyse 🗂️
• -dna — analyse DNA, and this is the default 🧬
• -rna — analyse RNA 🌿
• -protein — analyse protein 🫧
• -max — the maximum number of returned solutions 🔢
• -all — analyse both directions of the sequence ↔️
• -out — the name of the zip output file 🗜️
• -fasta — adds the fasta conversion of the matches to the result archive 📦
• -contig — sets the input bank as contig sequences 🧵
• -guid — a unique identifier for the query 🆔
• -email — the email address to send result availability info to (needs mail setup) 📧
• -local — use local mode (multi core) 💻
• -sge — use SGE mode 🌐
• -forcesplit — forces the sequence splitting according to your parameters, no matter how many models are used in the grammar ✂️

🌈 OTHER OPTIONS 🌈

• -lmax — the maximum length of a variable 📏
• -maxspacer — the maximum size of a spacer 🫧
• -noclean — don't delete the created files after treatment (this one's for debugging) 🐛
• -enabledups — enables duplicate result matches. by default, only singletons are kept 👯
• -filter — the type of filter to use when -enabledups is not enabled. allowed types are exact(default),local,local0,global 🎚️
• -lmin — the minimum length of a variable (speeds up parsing) ⚡
• -maxmatchsize — the maximum size of a match (speeds up parsing) ⚡
• -maxres — the maximum result size of a match (speeds up parsing) ⚡

🦋 AUTHOR 🦋

big credit to Olivier Sallou (olivier.sallou (at) irisa.fr) 👑 the legend behind all of this 💜

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that's the whole tea, bestie 🫶 LogolMultiExec version 1.0, dated September 28, 2011 🌸 stay iconic and keep those matches singleton-ed 💅✨