-
Notifications
You must be signed in to change notification settings - Fork 28
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Sai Chen
committed
Jun 15, 2019
1 parent
6a1863b
commit f912119
Showing
5 changed files
with
139 additions
and
144 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| # Installation of Paragraph | ||
|
|
||
| * [System Requirements](#SystemRequirements) | ||
| * [Hardware](#Hardware) | ||
| * [Operating systems](#Operatingsystems) | ||
| * [Third-party libraries](#ThirdPartyLibraries) | ||
| * [Static Build](#StaticBuild) | ||
| * [Installation](#Installation) | ||
| * [Native build](#NativeBuild) | ||
| * [From Docker image](#FromDockerImage) | ||
|
|
||
| ## <a name='SystemRequirements'></a>System Requirements | ||
|
|
||
| ### <a name='Hardware'></a>Hardware | ||
|
|
||
| A standard workstation with at least 8GB of RAM should be sufficient for compilation and testing of the program. | ||
|
|
||
| ### <a name='Operatingsystems'></a>Operating systems | ||
|
|
||
| Paragrpah is supported on the following systems: | ||
|
|
||
| - Ubuntu 16.04 and CentOS 5-7, | ||
| - macOS 10.11+, | ||
|
|
||
| Python 3.6+ is required. | ||
|
|
||
| We recommend using g++ (6.0+), or a recent version of Clang. | ||
|
|
||
| We use the C++11 standard, any Posix compliant compiler supporting this standard | ||
| should be usable. | ||
|
|
||
| ### <a name='ThirdPartyLibraries'></a>Third-party libraries | ||
|
|
||
| Please check [requirements](../requirements.txt) for required python modules. | ||
|
|
||
| We have included copies of other dependent libraries in external/. They are: | ||
| - Google Test and Google Mock (v1.8.0) | ||
| - Htslib (v1.9) | ||
| - Spdlog | ||
|
|
||
| ## <a name='Static Build'></a>Static Build | ||
|
|
||
| We provide a static build that works for GCC 5.2+ under linux environment. No installation is required for the static build. | ||
|
|
||
| Download the static build under "release" tag of the github repo. | ||
|
|
||
| ## <a name='Installation'></a>Installation | ||
|
|
||
| ### <a name='NativeBuild'></a>Native buid | ||
|
|
||
| [Boost libraries](http://www.boost.org) version >= 1.5 is required. | ||
| - We prefer to statically link Boost libraries to Paragraph executables: | ||
|
|
||
| ```bash | ||
| cd ~ | ||
| wget http://downloads.sourceforge.net/project/boost/boost/1.65.0/boost_1_65_0.tar.bz2 | ||
| tar xf boost_1_65_0.tar.bz2 | ||
| cd boost_1_65_0 | ||
| ./bootstrap.sh | ||
| ./b2 --prefix=$HOME/boost_1_65_0_install link=static install | ||
| ``` | ||
|
|
||
| - To point Cmake to your version of Boost use the `BOOST_ROOT` environment variable: | ||
|
|
||
| ```bash | ||
| export BOOST_ROOT=$HOME/boost_1_65_0_install | ||
| ``` | ||
|
|
||
| Once you have boost installed, checkout the repository like so: | ||
|
|
||
| ```bash | ||
| git clone https://github.com/Illumina/paragraph.git | ||
| cd paragraph-tools | ||
| ``` | ||
|
|
||
| Then create a new directory for the program and compile it there: | ||
|
|
||
| ```bash | ||
| # Create a separate build folder. | ||
| cd .. | ||
| mkdir paragraph-tools-build | ||
| cd paragraph-tools-build | ||
|
|
||
| # Configure | ||
| # optional: | ||
| # export BOOST_ROOT=<path-to-boost-installation> | ||
| cmake ../paragraph-tools | ||
| # if this doesn't work, run this instead: | ||
| # cmake ../paragraph-tools -DCMAKE_CXX_COMPILER=`which g++` -DCMAKE_C_COMPILER=`which gcc` -DBOOST_ROOT=$BOOST_ROOT | ||
|
|
||
| # Make, use -j <n> to use n parallel jobs to build, e.g. make -j4 | ||
| make | ||
| ``` | ||
|
|
||
| ### <a name='FromDockerImage'></a>From Docker Image | ||
| We also provide a [Dockerfile](Dockerfile). To build a Docker image, run the following command inside the source | ||
| checkout folder: | ||
|
|
||
| ```bash | ||
| docker build . | ||
| ``` | ||
|
|
||
| Once the image is built you can find out its ID like this: | ||
|
|
||
| ```bash | ||
| docker images | ||
| ``` | ||
| ``` | ||
| REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE | ||
| <none> <none> 54c7d4015330 16 seconds ago 1.76 GB | ||
| ``` | ||
|
|
||
| Check the below section for how to run Paragraph, and execute this before running: | ||
|
|
||
| ```bash | ||
| sudo docker run -v `pwd`:/data 54c7d4015330 | ||
| ``` | ||
|
|
||
| The current directory can be accessed as `/data` inside the Docker container. | ||
|
|
||
| The default entry point is `multigrmpy.py`. | ||
|
|
||
| To override the default entrypoint and get an interactive shell, run: | ||
|
|
||
| ```bash | ||
| sudo docker run --entrypoint /bin/bash -it 54c7d4015330 | ||
| ``` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters