Installation
Building from source
It may be necessary to install several system-level libraries to build odgi
.
On Ubuntu
, these can be installed using apt
:
sudo apt install build-essential cmake python3-distutils python3-dev libjemalloc-dev
Alternatively, after sudo apt install guix
start a GNU Guix build container with
source .guix-build
odgi
requires a C++ version of 9.3 or higher. You can check your version via:
gcc --version
g++ --version
If this requirement is satisfied, obtain a copy of the repository and its submodules:
git clone --recursive https://github.com/pangenome/odgi.git
cd odgi
Finally, build odgi
using cmake
:
cmake -H. -Bbuild && cmake --build build -- -j 2
The -j
argument determines the number of threads used for the compilation process. In the command above it is set to
2
. As odgi
is a fairly large project, it is recommended to set -j
to the maximum number of available threads. This
can reduce the compilation time significantly.
Note
If you need to avoid machine-specific optimizations, use the CMAKE_BUILD_TYPE=Generic
build type:
cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic && cmake --build build -- -j 3
BIOCONDA
odgi
recipes for Bioconda are available at https://bioconda.github.io/recipes/odgi/README.html. To install the latest version using Conda please execute:
conda install -c conda-forge -c bioconda odgi
GUIX
Installing via the guix-genomics git repository
First, clone the guix-genomics repository:
git clone https://github.com/ekg/guix-genomics
And install the odgi
package to your default GUIX environment:
GUIX_PACKAGE_PATH=. guix package -i odgi
Now ODGI is available as a global binary installation.
Installing via the guix-genomics channel
Add the following to your ~/.config/guix/channels.scm
:
(cons*
(channel
(name 'guix-genomics)
(url "https://github.com/ekg/guix-genomics.git")
(branch "master"))
%default-channels)
First, pull all the packages, then install odgi
to your default GUIX environment:
guix pull
guix package -i odgi
If you want to build an environment only consisting of the odgi
binary, you can do:
guix environment --ad-hoc odgi
For more details about how to handle Guix channels, please go to https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git.
Docker
Thanks to our Bioconda recipe https://bioconda.github.io/recipes/odgi/README.html a docker image is generated for free.
Pulling the latest odgi
docker image:
docker pull quay.io/biocontainers/odgi:<tag>
Please see odgi/tags for valid values for <tag>
.