Collaborative python library used in the DYOGEN team for studying the evolution of gene order in vertebrates.
The easiest way to install LibsDyogen is to execute the remote script INSTALL.sh hosted on github. This script will clone the github deposit itself. Dependencies will be installed with the package manager "apt-get" of debian distributions. LibsDyogen and its plugged softwares will be installed into /home/${USER}/Libs. The sudo password is required to
- Enable the universe deposit
- Install dependencies with apt-get
- Add LibsDyogen folder into PYTHONPATH, via an edition of ~/.bashrc
Install curl, if you don't have it
sudo apt-get update
sudo apt-get install curl
Use curl to execute the remote file INSTALL.sh hosted on github
bash <(curl -s https://raw.githubusercontent.com/DyogenIBENS/LibsDyogen/master/INSTALL.sh)
If it does not work follow the next instructions.
Core dependencies
- python 2.7
- cython
Marginal dependencies
- numpy
- scipy
- matplotlib
You also need git for cloning the git deposit.
Enable the deposit 'Universe' on debian/ubuntu distributions
sudo add-apt-repository universe
Install dependencies
sudo apt-get update
sudo apt-get install git python2.7 cython python-matplotlib python-scipy python-numpy
Depending on your distribution and version, you may need to change the names of packages
If this did not work, look at indications of authors
- matplotlib : https://matplotlib.org/users/installing.html
- scipy : https://www.scipy.org/install.html
- ...
Choose a path for the installation of the library and plugins. Here we choose /home//Libs.
PATH_PARENT_ALL="/home/${USER}/Libs"
Create the main folder for the installation
mkdir -p ${PATH_PARENT_ALL}
Clone the LibsDyogen library
PATH_LIBSDYOGEN="${PATH_PARENT_ALL}/LibsDyogen"
git clone https://github.com/DyogenIBENS/LibsDyogen ${PATH_LIBSDYOGEN}
Add the LibsDyogen root folder to the PYTHONPATH environment variable
echo "export PYTHONPATH=\"\${PYTHONPATH}:${PATH_LIBSDYOGEN}\"" >> ~/.bashrc
export PYTHONPATH=${PYTHONPATH}:${PATH_LIBSDYOGEN}
Cythonise *.pyx files (=compile C-like files)
bash ${PATH_LIBSDYOGEN}/cythonisePyxFiles.sh ${PATH_LIBSDYOGEN}
cd ${PATH_PARENT_ALL}
wget http://euler.slu.edu/~goldwasser/homologyteams/homologyteams-1.1.zip
unzip homologyteams-1.1.zip
cd homologyteams-1.1/src
Compile sources with gcc
make
Homolgyteams should now be plugged automatically to LibsDyogen. If it is not plugged, update the PATH_HOMOLOGYTEAMS_BIN variable in ${PATH_LIBSDYOGEN}/utils/myGeneTeams.py.
PATH_HOMOLOGYTEAMS_BIN = "<PATH_PARENT_ALL>/homologyteams-1.1/src/homologyteams"
with <PATH_PARENT_ALL> the appropriate path : in our case it's /home//Libs, with your user name.
cd ${PATH_PARENT_ALL}
wget http://bioinformatics.psb.ugent.be/downloads/psb/i-adhore/i-adhore-3.0.01.tar.gz
tar -zxvf i-adhore-3.0.01.tar.gz
rm i-adhore-3.0.01.tar.gz
Finish the installation
cd i-adhore-3.0.01
mkdir build
cd build
Cmake and g++ are needed for this step.
sudo apt-get install cmake
sudo apt-get install g++
If you don't already have them.
libpng and zlib are marginal dependencies of i-ADHoRe 3.0.
sudo apt-get install libpng-dev
sudo apt-get install zlib1g-dev
Depending on your distribution and version, you may need to change the names of packages libpng-dev and zlib1g-dev.
cmake ..
make
You do not need to install it, skip make install.
Verify that i-adhore is working
cd ../testset/datasetI
../../build/src/i-adhore datasetI.ini
i-adhore should be plugged automatically to LibsDyogen. If it is not plugged properly, update the PATH_ADHORE_BIN variable in ${PATH_LIBSDYOGEN}/utils/myADHoRe.py.
PATH_ADHORE_BIN = "<PATH_PARENT_ALL>/i-adhore-3.0.01/build/src/i-adhore"
with <PATH_PARENT_ALL> the appropriate path : in our case it's /home//Libs, with your user name.
cd ${PATH_PARENT_ALL}
Download cyntenator sourcefiles (located in the folder https://www.bioinformatics.org/cyntenator/wiki/Main/HomePage)
wget -r -np -nH --cut-dirs=3 -R index.html https://bbc.mdc-berlin.de/svn/bioinformatics/Software/cyntenator/
cd cyntenator
Compile
g++ -Wno-deprecated cyntenator.cpp localign.cpp genome.cpp flow.cpp species_tree.cpp -o cyntenator
Verify that Cyntenator is working. Read the INSTALL file to find tests to check the installation, for instance try
./cyntenator -t "(HSX.txt MMX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5):1" > human_mouse
Cyntenator should be plugged automatically to LibsDyogen. If it is not plugged, update the PATH_CYNTENATOR_BIN variable in ${PATH_LIBSDYOGEN}/utils/myCyntenator.py
PATH_CYNTENATOR_BIN = "<PATH_PARENT_ALL>/cyntenator/cyntenator"
with <PATH_PARENT_ALL> the appropriate path : in our case it's /home//Libs, with your user name
See each main in python modules for usage.
This folder contains several scripts that edit, convert species tree, gene trees or gene families.
Convert nhx (or .nwk, newick) gene trees to our tabular format (phylTree)
scripts/nhxGeneTrees2phylTreeGeneTrees.py data/geneTrees.example.nhx > res/geneTrees.protTree
Convert a newick species tree into a phylTree species tree
scripts/newickSpeciesTree2phylTreeSpeciesTree.py data/speciesTree.nwk > res/speciesTree.phylTree
Extract families from gene trees
scripts/familiesFromGeneTrees.py res/speciesTree.phylTree res/geneTrees.protTree -out:families=res/%s.families.bz2 > res/geneTreesAfterExtractingFamilies.protTree
These families files define gene families. All descendant genes of the same ancestral gene belong to the same family. .families.bz2 contains gene families that derive from a unique gene in the genome.
Usually, when a set of species is considered, each gene family is defined as the set of genes deriving from the same ancestral gene of the most recent common ancestor.
If you want to keep LibsDyogen up to date, execute
cd ${PATH_LIBSDYOGEN}
git pull
often.
This will upgrade your local git deposit to the last commit.
If you want a more stable version, after git pull, you can downgrade to the latest tagged version (=stable release), just execute
- Get tags from the github deposit:
git fetch --tags - Get the latest tag name
latestTag=$(git describe --tags `git rev-list --tags --max-count=1`) - Checkout the latest tag:
git checkout $latestTag
After git fetch --tags, you can also switch to any anterior tagged version
- List all tagged versions:
git tag -l - Checkout to the version you want:
git checkout <tagName>
If you want to contribute to this deposit please
- Fork it
- Create your feature branch:
git checkout -b my-new-feature - Commit your changes:
git commit -am 'Add some feature' - Push to the branch:
git push origin my-new-feature - Submit a pull request
- Matthieu Muffato: started the library and created: myGenomes, myTools, myPsOutput, myProteinTre, myPhylTree, myKaryoDrawer, myFile, myGenomes, myGraph, myMultiprocess, myMaths
- Joseph Lucas: Updated the library and organised it, created: myDiags, myLightGenomes, myCondor, myGeneTeams, myGenomesDrawer, myIntervals, myMapping, myProbas, mySvgDrawer and updated: myTools
- Nga thi thuy Nguyen: Updated some functions of myDiags and myGraph
- Lucas Tittmann: Updated some functions of myDiags
- Hugues Roest Crollius: supervisor
This code may be freely distributed and modified under the terms of the GNU General Public License version 3 (GPL v3) and the CeCILL licence version 2 of the CNRS. These licences are contained in the files:
- LICENSE-GPL.txt (or http://www.gnu.org/licenses/gpl-3.0-standalone.html)
- LICENCE-CeCILL.txt (or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html)
Copyright for this code is held jointly by the Dyogen (DYnamic and Organisation of GENomes) team of the Institut de Biologie de l'Ecole Normale Supérieure (IBENS) 46 rue d'Ulm Paris, and the individual authors.