Commit c3b53c47 authored by DURAND Patrick's avatar DURAND Patrick
Browse files

update 1.3.0 doc

parent bcd902c3
......@@ -10,16 +10,16 @@
--------------------------------------------------------------------------------
# What is GATB ?
# What is GATB?
GATB is made of two master projects:
* The **GATB-CORE project** provides a set of highly efficient algorithms to analyse NGS data sets. These
methods enable the analysis of data sets of any size on multi-core desktop computers, including very
huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and
even complex samples (e.g. metagenomes). Read more about GATB at <a href="https://project.inria.fr/gatb/">https://project.inria.fr/gatb</a>.
even complex samples (e.g. metagenomes). Read more about GATB at <a href="https://gatb.inria.fr/">https://gatb.inria.fr/</a>.
* The **GATB-TOOLS project** contains a set of ready-to-use softwares relying on GATB-CORE algorithms. You can have a look at available tools at <a href="https://project.inria.fr/gatb/software/">https://project.inria.fr/gatb/software</a>.
* The **GATB-TOOLS project** contains a set of ready-to-use softwares relying on GATB-CORE algorithms. You can have a look at available tools at <a href="https://gatb.inria.fr/software/">https://gatb.inria.fr/software/</a>.
--------------------------------------------------------------------------------
# What is GATB-CORE ?
......@@ -48,14 +48,9 @@ GATB-Core natively provides the following operations:
* graph simplifications for assembly (tip removal, bulge removal)
By itself GATB-CORE is not an NGS data analysis tool. However, it can be
used to create such tools; see below section called 'How to quickly create a project based on gatb-core ?'.
used to create such tools; see section [Quickly create a new GATB-TOOL software](#Quickly create a new GATB-TOOL software), below.
They already exist a set of ready-to-use tools relying on GATB-CORE library: see [https://project.inria.fr/gatb/software/](https://project.inria.fr/gatb/software/)
# License
GATB is free software; you can redistribute it and/or modify it under the Affero GPL v3
license. See http://www.gnu.org/licenses/agpl-3.0.en.html
They already exist a set of ready-to-use tools relying on GATB-CORE library: see [https://gatb.inria.fr/software/](https://gatb.inria.fr/software/)
# Project content
......@@ -64,29 +59,73 @@ generate the wanted artifacts:
* dynamic and static libraries holding the services component
* unit tests of the component
* 120+ unit tests of the entire library
# Dependencies
The following third parties have to be already installed to compile GATB-Core:
# Compiling GATB-CORE
* a **C++/11 capable compiler** (*e.g.* gcc 4.7+, clang 3.5+, Apple/clang 6.0+)
* **CMake 3.1+**
Since the compilation is based on CMake (release 2.6+), a common way to build all the artifacts is:
In addition, you could install these optional tools:
* **doxygen**: to compile a local copy of the GATB-Core documentation
* **cppunit**: to compile and run Unit tests
# Compile GATB-CORE
## Compile in Release mode (default)
Type:
cd <some_directory>
git clone https://github.com/GATB/gatb-core.git
cd gatb-core/gatb-core
mkdir build ; cd build ; cmake .. ; make
mkdir build ; cd build ; cmake .. ; make -j8
Unit tests (requires cppunit) can also be executed to check the integrity of the library on your system:
## Compile in Debug mode
Type save as above, except for the CMake command:
cmake -D CMAKE_BUILD_TYPE=Debug ..
make -j8
## Run unit tests
* cppunit is required
* compile using the command above (Release or Debug mode)
Then type:
# enter gatb-core build directory
cd gatb-core/gatb-core/build
make test
# set verbose mode to on so that we have name of failing tests (if any)
export CPPUNIT_VERBOSE=1
# Copy database for unit tests
cp -r ../test/db ./test/
# Launch the full test suite
cd bin
./gatb-core-cppunit
The gatb-core-cppunit command may also take as argument the categories of tests that show up in the verbose output, e.g. './gatb-core-cppunit TestBank'.
More about GATB-CORE code compiling instruction is available [here](http://gatb-core.gforge.inria.fr/doc/api/compilation.html).
# Work on GATB-Core code using Eclipse
Read [this documentation](https://gatb.inria.fr/use-eclipse-to-develop-gatb-core-softwares/).
# GATB-Core programming tutorial
You can follow [this link](https://gatb.inria.fr/gatb-programming-tutorial/) to start the GATB-Core Online Tutorial trail.
# Documentation
API documentation is available [here](http://gatb-core.gforge.inria.fr/doc/api/).
The complete GATB-Core documentation is available [here](http://gatb-core.gforge.inria.fr/doc/api/). It contains: API, code snippets, compile instructions, *etc*.
Nevertheless, you can create a local copy of the documentation as follows (we suppose you already compiled the c++ code, see above; requires 'doxygen'):
......@@ -113,15 +152,6 @@ Tools may set a default kmer lists in their CMakeFiles.txt, as such (see for ins
list (APPEND KSIZE_DEFAULT_LIST 32 64 96 128 160 192 224 256)
--------------------------------------------------------------------------------
# Dependencies
The following third parties should be already installed:
* cmake (mandatory)
* doxygen
* cppunit
--------------------------------------------------------------------------------
# Directory content
......@@ -159,22 +189,30 @@ For one atomic package (or sub package), we should have:
* directory 'impl' several implementations of the API
--------------------------------------------------------------------------------
# How to quickly create a project based on GATB-CORE ?
# Quickly create a new GATB-TOOL software
A GATB-TOOL is a new software relying upon GATB-CORE.
You use GATB-CORE by creating a new tool project, with the following script:
You use GATB-CORE to create a new tool project, with the following script:
sh scripts/NewProject/NewProject.sh -d directory -n toolName
sh scripts/NewProject/NewProject.sh -d directory -n toolName
where 'directory' is the directory where the project will be created and 'toolName' is the name of the project.
The script will automatically creates the full path directory/toolName to deploy a self-contained tool.
where:
'directory' is the directory where the project will be created
'toolName' is the name of the project.
The script will automatically creates the full path 'directory/toolName' to deploy a self-contained tool.
By default, the following part will be included in the project:
* a CMakeLists.txt file used for building the project
* a 'tools' directory holding a default source code using GATB-Core
* a 'scripts' directory holding a script to automatically package the tool
* an optional 'thirdparty' directory holding the gatb-core resources
* a CMakeLists.txt file used for building the project
* a 'tools' directory holding a default source code using GATB-Core
* a 'scripts' directory holding a script to automatically package the tool
* an optional 'thirdparty' directory holding the gatb-core resources
The 'thirdparty' directory is only available for tool created outside the GATB-Tools repository.
Tools located within GATB-Tools rely on a common GATB-CORE sub-module already available in this repository.
The directory where the project is created has no link to any external resources. You can therefore
......@@ -184,33 +222,14 @@ Such a project can be a start for building applications based on GATB-CORE.
More on creating a new GATB-Core based project: [http://gatb-core.gforge.inria.fr/doc/api/new_project.html](http://gatb-core.gforge.inria.fr/doc/api/new_project.html)
----------------------------------------------------------------------------------
# Notes for GATB-core developers
## To compile in debug mode
Type:
mkdir build ; cd build
cmake cmake -D CMAKE_BUILD_TYPE=Debug .. ..
make -j4
## To work on GATB-Core code using Eclipse
Read [this documentation](https://gatb.inria.fr/use-eclipse-to-develop-gatb-core-softwares/).
## To run unit tests
* compile using the command above
* then type:
bin/gatb-core-cppunit
One may set the environment variable CPPUNIT_VERBOSE to 1 to known which tests pass.
#Contact
The gatb-core-cppunit command may also take as argument the categories of tests that show up in the verbose output, e.g. 'bin/gatb-core-cppunit TestBank'.
To contact a developer, request help, *etc*, use:
https://gatb.inria.fr/contact/
#Contact
# License
To contact a developer, request help, etc: https://gatb.inria.fr/contact/
\ No newline at end of file
GATB is free software; you can redistribute it and/or modify it under the [Affero GPL v3 license](http://www.gnu.org/licenses/agpl-3.0.en.html).
\ No newline at end of file
......@@ -205,6 +205,14 @@
*
* Note: the script re-built the entire tool from its sources to ensure a clean build process.
*
* \section use_eclipse2 Use Eclipse c++ IDE to work on a GATB-TOOL
*
* If you are interested in using an IDE to develop c++ source codes relying on the
* GATB-Core library, we have written this manual to explain how to setup Eclipse
* c++ framework:
*
* <a href="https://gatb.inria.fr/use-eclipse-to-develop-gatb-core-softwares/">https://gatb.inria.fr/use-eclipse-to-develop-gatb-core-softwares/</a>
*
************************************************************************************
************************************************************************************
* \page snippets_iterators Iterators snippets
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment