biowasm

WebAssembly modules for common genomics utilities, including:

samtools v1.10 (and htslib)
bedtools v2.29
fastp v0.20.1
seqtk v1.3
wgsim
bhtsne
seq-align

Usage

For convenience, biowasm modules are compiled to WebAssembly and hosted on cdn.sandbox.bio.

For a simple starter example, see Aioli.

Setup

# Emscripten version to use (most tools were tested with 1.39.1)
TAG=1.39.1

# Fetch Emscripten docker image
docker pull robertaboukhalil/emsdk:$TAG

# Create the container and mount ~/wasm to /src in the container
docker run \
    -dt \
    -p 12345:80 \
    --name wasm \
    --volume ~/wasm:/src \
    robertaboukhalil/emsdk:$TAG

Compile a tool

# Go into your container
docker exec -it wasm bash

# Compile seqtk
cd biowasm/
make seqtk

# This will create tools/<tool name>/build with .js/.wasm files
ls tools/seqtk/build

Contribute new tool

First, add the tool as a git module:

# Fetch codebase
mkdir -p tools/seqtk
git submodule add https://github.com/lh3/seqtk.git tools/seqtk/src

# Get specific version of the tool
cd tools/seqtk/src
git checkout v1.3
cd -

# Stage changes for git
git add tools/seqtk/src .gitmodules

You should also create the following files:

tools/<tool>/
    README.md   Details about the tool and dependencies
    compile.sh  Script that will run to compile the tool to WebAssembly (can use `$EM_FLAGS` for common flags)
    patch       Patches that need to be applied to the code to compile it to WebAssembly (optional)

Todo

Add tests
Add support for compiling bioinformatics tools written in Rust such as sourmash and rust-bio

philiptzou / biowasm