GBrowse2(1)

💖 GBrowse2(1) — USER COMMANDS ✨

okay bestie, sit down, hydrate, and let me tell you about GBrowse2, aka The Generic Genome Browser 🧬👑 — this is the GBrowse2(1) manual page and I am so excited to walk you through it.

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🌸 NAME 🌸

GBrowse2 — the Generic Genome Browser, fr fr. it's THE genome browser. iconic behavior only 💅

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🎀 SYNOPSIS 🎀

libgbrowse-perl [-h]

that's it. that's the whole vibe. 💖

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✨ INSTALLATION ✨

so if Apache2 is already on the system, the software has already gone ahead and configured it to link URLs to GBrowse directories. slay 💅 but — and this is the part everyone forgets — you need to restart Apache for it to actually take it into account. no restart, no glory.

the configuration lives in the file /etc/gbrowse2/apache2.conf. 🗂️

if you're using another web server instead? no worries bestie, just go refer to the apache2 template and map urls in the same way. copy the assignment, basically. 📝

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🦋 DEPENDENCIES 🦋

there are additional optional perl dependencies hanging around that unlock extra features. it's giving "downloadable content" energy, ngl. if you want the deets, go refer to Optional modules in the INSTALL file. 🍓

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💜 CONFIGURATION 💜

the gbrowse2 configuration files live in /etc/gbrowse. 📁

the main configuration file is GBrowse.conf, and it's the one holding all the global configuration elements — the main character of configs, honestly.

specific configuration files are located in the same directory, one per data bank. so like, per data bank, one file, same folder, we love organization. 🌈

for more details, one should refer to the GBrowse documentation. and guess what — the installation ships with a Yeast genome sample, so you have something to play with immediately. yeast! 🍞✨

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💖 DESCRIPTION 💖

GBrowse is a simple but highly configurable web-based genome browser. it's a component of the Generic Model Organism Systems Database project (GMOD). 🧬

some of its features, because you know I'm gonna list them all:

• Simultaneous bird's eye and detailed views of the genome 👀🔍
• Scroll, zoom, center 🖱️
• Attach arbitrary URLs to any annotation 🔗
• Order and appearance of tracks are customizable by administrator and end-user 🎨
• Search by annotation ID, name, or comment 🔎
• Supports third party annotation using GFF formats 🧾
• Settings persist across sessions 💾 (it remembers you, bestie)
• DNA and GFF dumps 📤
• Connectivity to different databases, including BioSQL and Chado 🗄️
• Multi-language support 🌍
• Third-party feature loading 📦
• Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features) 🔥

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🌈 WEB ACCESS 🌈

GBrowse is accessible at URL http://localhost/gbrowse2 🌐

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👑 AUTHOR 👑

• Olivier Sallou (olivier.sallou (at) irisa.fr) — Man page and packaging
• Lincoln Stein — GBrowse

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that's the whole page, bestie. every flag, every path, every feature, zero skips. no cap. 🫶

version 1.1.0 · February 07, 2011 — mwah, go forth and browse some genomes 💅🧬✨