diff --git a/CMakeLists.txt b/CMakeLists.txt index a8298bab..07feff3b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,8 +2,8 @@ cmake_minimum_required (VERSION 2.8) project (vcf-validator CXX C) set (vcf-validator_VERSION_MAJOR 0) -set (vcf-validator_VERSION_MINOR 9) -set (vcf-validator_VERSION_PATCH 7) +set (vcf-validator_VERSION_MINOR 10) +set (vcf-validator_VERSION_PATCH 0) configure_file ( "${PROJECT_SOURCE_DIR}/inc/cmake_config.hpp.in" diff --git a/README.md b/README.md index 56e10558..10efd6da 100644 --- a/README.md +++ b/README.md @@ -13,11 +13,11 @@ These tools have been implemented using C++11. ### From Binaries -The vcf-validator is built with all the dependencies included. It can be downloaded directly from the [latest release](https://github.com/EBIvariation/vcf-validator/releases) for the most stable experience using vcf-validator. Along with the release notes, you will find the executables `vcf_validator` and `vcf_assembly_checker` for Linux, macOS and Windows. For Windows, please also download the libraries in the [lib/windows_specific/](https://github.com/EBIvariation/vcf-validator/tree/master/lib/windows_specific/) folder. +The vcf-validator is built with all the dependencies included. It can be downloaded directly from the [latest release](https://github.com/EBIvariation/vcf-validator/releases) for the most stable experience using vcf-validator. Along with the release notes, you will find the executables `vcf_validator` and `vcf_assembly_checker` for Linux, macOS and Windows. ### From conda -Starting from [v0.9.6](https://github.com/EBIvariation/vcf-validator/releases/tag/v0.9.6), you can install vcf-validator via conda using +Starting from [v0.9.6](https://github.com/EBIvariation/vcf-validator/releases/tag/v0.9.6), you can install vcf-validator on Linux and Mac via conda using. ``` conda install -c bioconda vcf-validator @@ -54,10 +54,6 @@ Each report is written into its own file and it is named after the input file, f A flag for validating evidence can be passed with `--require-evidence`. This will validate whether the VCF includes either Genotypes or Allele Frequencies. This flag will be **false** by default. -### Debugulator - -Removed debugulator support and ODB dependency. - ### Assembly Checker vcf-assembly-checker assesses the correctness of a VCF file with respect to a FASTA file (that should contain the reference sequence). The assembly checker reads the CHR, POS and REF columns from the VCF, and for each line, looks into the FASTA file to see if the REF allele matches that region. A VCF file is considered valid if all the variants match the sequence in the FASTA file. @@ -139,7 +135,7 @@ If you are using Ubuntu 16, you can prepare all dependencies and compile the Val ``` sudo apt-get install cmake wget build-essential ./install_dependencies.sh linux -mkdir build && cd build && cmake -G "Unix Makefiles" .. +mkdir build && cd build && cmake -G "Unix Makefiles" -DSTATIC_BUILD=1 .. make ``` @@ -148,7 +144,7 @@ The VCF Validation Suite binaries will be created in the `build/bin` subfolder. ##### CMake and automatic installation The automatic install **requires** CMake and wget to be installed before running the script (as zlib require them to be installed). Also, the script will compile some dependencies so a compilation environment is needed. If you are using Ubuntu, you can install all that with the command `sudo apt-get install cmake wget build-essential`. After installing that, use the command `./install_dependencies.sh linux`. -A subfolder named `linux_dependencies` will be created, with all the required libraries copied into it. +A subfolder named `dependencies` will be created, with all the required libraries copied into it. ##### Boost @@ -157,10 +153,6 @@ A subfolder named `linux_dependencies` will be created, with all the required li The dependencies are the Boost library core, and its submodules: Boost.filesystem, Boost.iostreams, Boost.program_options, Boost.regex, Boost.log and Boost.system. If you are using Ubuntu, you can install them with the command `sudo apt-get install libboost-dev libboost-filesystem-dev libboost-iostreams-dev libboost-program-options-dev libboost-regex-dev libboost-log-dev`. -##### ODB - -ODB dependency is removed, ODB and debugulator are no longer in build. - #### Compile In order to create the build scripts, please run `cmake` with your preferred generator. For instance, `mkdir build && cd build && cmake -G "Unix Makefiles" ..` will create Makefiles, and to build the binaries, you will need to run `make`. @@ -186,7 +178,6 @@ Boost | \>=1.65 | manual You can prepare all dependencies and compile the Validation Suite with these commands: ``` brew install cmake boost sqlite3 -./install_dependencies.sh osx mkdir build && cd build && cmake -G "Unix Makefiles" .. make ``` @@ -226,10 +217,6 @@ bootstrap * Add boost_1_xx_x/stage/lib folder to the environment variable `LIB` * Add boost_1_xx_x folder to the environment variable `INCLUDE` -##### ODB - -ODB dependency is removed, ODB and debugulator are no longer in build. - #### Compile In order to create the build scripts and compile vcf-validator, please run the following commands from the project root folder: