Commit 751992b2 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'update-doc' into 'dev'

Update doc

See merge request !249
parents 757185a9 6fa2d566
Pipeline #32997 passed with stages
in 52 seconds
......@@ -45,7 +45,7 @@ can manage, upload, analyze and annotate their runs directly on the web applicai
- Stable releases can be downloaded from http://bioinfo.lille.inria.fr/vidjil
- Development code is under [[algo/]]
- Documentation, compilation and installation instructions: [[doc/algo.org]]
- Documentation, compilation and installation instructions: [[doc/vidjil-algo.md]]
** The web application
......
......@@ -69,8 +69,7 @@ Vidjil-algo has been successfully tested on the following platforms :
- OS X 10.9, 10.10, 10.11
Vidjil-algo is developed with continuous integration using systematic unit and functional testing.
The development team internally uses [Jenkins](https://jenkins-ci.org/) for that.
Moreover, the results of some of these tests can be publicly checked on [travis-ci.org](https://travis-ci.org/vidjil/vidjil).
The development team internally uses [Gitlab CI](http://gitlab.vidjil.org/pipelines) and [Jenkins](https://jenkins-ci.org/) for that.
## Build requirements (optional)
......@@ -79,7 +78,7 @@ You can also download a static binary (see next paragraph, 'Installation').
To compile Vidjil-algo, make sure:
- to be on a POSIX system ;
- to have a C++11 compiler (as `g++` 4.8 or above, `g++` 7.3 being supported, or `clang` 3.3 or above).
- to have a C++11 compiler (as `g++` 4.8 or above, or `clang` 3.3 or above).
- to have the `zlib` installed (`zlib1g-dev` package under Debian/Ubuntu,
`zlib-devel` package under Fedora/CentOS).
......@@ -114,7 +113,7 @@ At the time of redacting the documentation, `g++` requires extra options to
ensure flawless compilation and execution of Vidjil-algo:
``` bash
make MAKE=gmake CXXFLAGS="-D_GLIBCXX_USE_C99 -Wl,-rpath=/usr/local/lib/gcc49"
make MAKE=gmake CXXFLAGS="-std=c++11 -O2 Wall -D_GLIBCXX_USE_C99 -Wl,-rpath=/usr/local/lib/gcc49"
```
The `gcc49` at the end of the command line is to be replaced by the `gcc` version
......@@ -190,27 +189,12 @@ make demo # download demo files (S22 and L4, see demo/get-sequenc
./vidjil-algo -h # display help/usage
```
If your build system does not use C++11 by default, you should replace the `make` commands by:
On some older systems you may need to replace the `make` commands with:
``` bash
make CXXFLAGS='-std=c++11' ### gcc-4.8
make CXXFLAGS='-std=c++11' LDFLAGS='-stdlib=libc++' ### OS X Mavericks
make LDFLAGS='-stdlib=libc++' ### OS X Mavericks
```
### Package
If you use a Debian-based operating system you can simply add the Vidjil
repository to your sources.list:
deb <http://rby.vidjil.org:8080/archive> sid/all/
deb <http://rby.vidjil.org:8080/archive> sid/amd64/
deb <http://rby.vidjil.org:8080/archive> wheezy/all/
deb <http://rby.vidjil.org:8080/archive> wheezy/amd64/
And install from he command line:
apt-get update
apt-get install vidjil
## Self-tests (optional)
You can run the tests with the following commands:
......
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