Installation

Install ucircfull binary release

wget https://github.com/YueqiJin/ucircfull/releases/download/v1.1.2/ucircfull-1.1.2-Linux.tar.gz
tar -xzf ucircfull-1.1.2-Linux.tar.gz
/path/to/ucircfull-1.1.2-Linux/bin/ucircfull --help

Install ucircfull from source code

Dependencies

  • cmake >= 3.4

  • make

  • g++ with C++23 support (GCC >= 13 recommended)

  • gcc with C++23 support (GCC >= 13 recommended)

  • libboost-all-dev

  • libseqan3-dev >= 3.4.0

  • libseqan2-dev

  • minimap2

  • rust

  • porechop

  • seqkit

  • samtools

Build ucircfull from source code

git clone https://github.com/yangence/ucircfull.git
cd ucircfull
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build -j

Install ucircfull to a deployment prefix

cmake --install build --prefix /opt/ucircfull

This installs executables to /opt/ucircfull/bin and shared libraries to /opt/ucircfull/lib.

Run ucircfull in apptainer

apptainer pull docker://jinyueqi/ucircfull
apptainer exec /path/to/ucircfull-latest.sif ucircfull --help

Required files

Users can prepare the external files under the following instructions:

  1. Indexed genome fasta file

samtools faidx $genome

  1. gene annotation GTF file