INSTALLATION

Fast installation

make all  
sudo make install  

More

• make clean ==> cleanup the repository and reset the original state
• sudo make uninstall ==> uninstall executables from the $PATH
• sudo make force_install ==> overwriting old link in $PATH

List of softwares

Executable	Descrition
gwEvol-paml	Run Positive selection model via PAML
gwEvol-result	Run all scripts to get the report and the analyze of a positive selection analysis

Usage

For help run executable with -h or --help

Controling jobs execution

Error during job completion related to the scheduler work

# number of model tested
model=5 
expected=$(echo "3+2*$model" |bc)

for pbs in $(ls schd/gwEvol_paml_*) ; do echo "$pbs" ; status=""; for dir in $(more $pbs | grep 'ete3 evol' | cut -f 1 -d ';' | cut -f 2 -d ' ' | uniq ) ; do status="${status}$(ls $dir | wc -l):" ; done ;echo "$status" ;done | grep -P ':(?!'"$expected"')\d+' -B 1 --no-group-separator 

Error during the job completion related to the job script

for errFile in $(find -name '*.err') ; do [[ -s $errFile ]] && echo $errFile >> errFile.list; done

Dependencies

• Python 2.7 (or higher but never tested)
  • upype
• R
  • markdown
  • ggplot2
  • knitr
• ete3 ( easy to install with conda )
• PAML
• TORQUE or SLURM scheduler PBS compatible

LICENCE

All files in this repository are authored by Julien FOURET and licenced under the GNU Public Licence v3.0

This work have been done during a PhD fellowship co-funded by ViroScan3D and the DGA (Direction Générale de l'Armement) in the context of a CIFRE-Défense

/*
 *   gwEvol use the MCSA database to perform 
 *   genome-wide positive selection analysis. 
 *   
 *   Copyright (C) 2018  Julien Fouret
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */