fgprimer

A Scala Library for primer design and related activities for genomic assays.

This readme document is mostly for developers/contributors and those attempting to build the project from source.

Detailed developer documentation can be found here.

• Overview
• Building
• Command line
• Include fgprimer in your project
• Contributing
• Authors
• License

Overview

Fgprimer is a Scala library and set of command line tools for primer design for genomic assay design. The collection of tools and associated API within fgprimer are used by our customers and others both for ad-hoc data analysis and within production pipelines.

Building

Cloning the Repository

To clone the repository: git clone https://github.com/fulcrumgenomics/fgprimer.git

Dependencies

primer3 (version 2.5.0 or greater) is a dependency. Note that starting with version 2.5 the primer3 config directory is no longer needed as the thermodynamic parameters are packaged into the binaries! Install from source or with conda: conda install -c bioconda primer3

A custom bwa is a dependency. Install it from source or with:

git clone -b interactive_aln git@github.com:fulcrumgenomics/bwa.git
cd bwa
make -j 12

Running the build

fgprimer is built using sbt.

Use sbt assembly to build an executable jar in target/scala-2.13/.

Tests may be run with sbt test.

Java SE 8 is required.

Include fgprimer in your project

You can include fgprimer in your project using the latest release (not currently available):

"com.fulcrumgenomics" %% "fgprimer" % "0.0.1"

for the latest released version or (buyer beware):

"com.fulcrumgenomics" %% "fgprimer" % "0.0.1-<githash>-SNAPSHOT"

for the latest development snapshot.

Contributing

Contributions are welcome and encouraged. We will do our best to provide an initial response to any pull request or issue within one-week. For urgent matters, please contact us directly.

Authors

• Tim Fennell (maintainer)
• Nils Homer (maintainer)

License

fgprimer is open source software released under the MIT License.