IGV-ScanFold

Patched version of IGV that integrates ScanFold functionality.

Run

IGV-ScanFold requires Python 3.

Windows

A pre-built version is available on releases.

Mac (10.15+, x86_64)

A pre-built version is available on releases.

Please open the Terminal app and run the following to download and run it.

cd ~/Downloads/
curl -L -O https://github.com/ResearchIT/IGV-ScanFold/releases/download/v0.2.3/IGV-ScanFold-macos-v0.2.3.zip
unzip IGV-ScanFold-macos-v0.2.3.zip
open -a IGV-ScanFold.app

Linux

Follow instructions to compile. Then

1. ./scripts/run_igv.sh

Compile

Requirements

OSX

• X-code cli tools
• python3
• jdk 11 (newer may work, haven't tested)

Linux

• python3
• jdk 11 (newer may work, haven't tested)

on fedora

sudo dnf install git zip patch java-11-openjdk.x86_64 gcc g++ python3-devel zlib-devel tar make

Build IGV (CI currently only does this)

1. clone this repository recursively
   git clone --recursive https://github.com/ResearchIT/IGV-ScanFold.git
2. ./scripts/apply_patch.sh
3. ./scripts/build_igv.sh

Build ScanFold and dependencies

1. ./scripts/build_scanfold_env.sh
2. ./scripts/build_viennarna.sh
   this may fail at src/Kinfold, but that's fine
3. ./scripts/build_rnastructure.sh

Links to IGV-ScanFold User Walkthroughs

1. https://structurome.bb.iastate.edu/igv-scanfold-supplemental-data
2. https://www.youtube.com/playlist?list=PL-FLz2olO5ubN8hKbeccZ6rfwBjfmTSyv