diff --git a/README.md b/README.md index ef1aac5..005cf27 100644 --- a/README.md +++ b/README.md @@ -1,37 +1,36 @@ # FragGeneScan++ -An improved version of [FragGeneScan-Plus][fgsp]. -## Installing -To build/install FragGeneScan++ from source, you will need [Meson][meson]. run the following commands from the source -repository: +A modified fork of [FragGeneScan-Plus][fgsp]. -```sh -meson build -ninja -C build -sudo ninja -C build install -``` -## Running -An example usage of FragGeneScan++ looks like the following: +## Installation -``` -FGS++ -s example/NC_000913-454.fna -o output -w 0 -t 454_5 -p 16 -``` +The installation instruction from [FGS+][fgsp install] remain valid: -For more info or a list of all options, run FragGeneScan++ without arguments. +1. Install `make` and `gcc`. + +2. Clone this repository and go to the repository root. + + ```sh + git clone https://github.com/unipept/FragGeneScanPlusPlus.git + cd FragGeneScanPlusPlus + ``` + +3. Run `make`. -## Documentation -To get the most recent version of the documentation, issue the following -command: + +## Running + +An example usage of FragGeneScan++ looks like the following: ``` -ninja -C build docs +FGSpp -s example/NC_000913-454.fna -o output -w 0 -t 454_5 -p 16 ``` -The documentation can then be viewed by opening `build/doc/html/index.html` in -your favorite browser. +For more info or a list of all options, run FragGeneScan++ without arguments. ### Output files + Upon completion, FragGeneScan++ can generate 3 files: * The `[output_file].faa` file lists amino acid sequences in FASTA format @@ -45,7 +44,9 @@ file consists of 5 columns ( _start position_, _end position_, _strand_, _frame_, and _score_). This file is not automatically generated: to obtain this file, set the `-e` flag to 1. + ## License + FragGeneScan++ is released under under the terms of the GNU General Public License, version 3 (or any later version), as published by the Free Software Foundation. @@ -55,3 +56,4 @@ Please see the [LICENSE](LICENSE) file for further information. [fgsp]: https://github.com/hallamlab/FragGeneScanPlus/ [meson]: https://mesonbuild.com/ +[fgsp install]: https://github.com/hallamlab/FragGeneScanPlus/wiki#setup-and-dependencies-1