Augur Auspice NextStrain - quipupe/from-assembly-to-nextstrain GitHub Wiki

Instalar programas

Por fa actualicemos esto con conda tambien

mafft

https://mafft.cbrc.jp/alignment/software/installation_without_root.html

wget https://mafft.cbrc.jp/alignment/software/mafft-7.471-with-extensions-src.tgz

Descomprimir la carpeta e instalarlo, prefiero que no se use el root pues muchas PC no tendran este permiso.

IQTREE

wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz

El ejecutable se encuentra en una carpeta bin

Para que el sistema reconozca los ejecutables siempre hay que jugar con el archivo .bashrc pero con cuidado

nano ~/.bashrc
export PATH=$PATH:/direcciondelejecutable
source ~/.bashrc

pip

pip hace que python3 instale todo mas facil

sudo apt-get install python3-pip

augur

python3 -m pip install nextstrain-augur

Esto hay que revisarlo por si no tenemos root

WARNING: The scripts f2py, f2py3 and f2py3.8 are installed in '/home/pipo/.local/bin' which is not on PATH. 
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.                                                   
WARNING: The scripts jupyter, jupyter-migrate and jupyter-troubleshoot are installed in '/home/pipo/.local/bin' which is not on PATH.                               
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.                                                   
WARNING: The script jupyter-trust is installed in '/home/pipo/.local/bin' which is not on PATH.                                                                     
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.                                                   
WARNING: The scripts snakemake and snakemake-bash-completion are installed in '/home/pipo/.local/bin' which is not on PATH.                                         
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.                                                   
WARNING: The script augur is installed in '/home/pipo/.local/bin' which is not on PATH.                                                                             
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

pondre /home/pipo/.local/bin en mi PATH

Auspice

https://nextstrain.github.io/auspice/introduction/install#installing-from-source

sudo apt install npm
npm install auspice
#si no funciona usar npm install auspice
#si aun asi no funciona intentar curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash - y luego sudo apt-get install -y nodejs
#Igual me dio errores en una de mi compu pero el programa instaló, creo que lo mejor es hacerlo todo via conda
luego poner esta carpeta en el PATH

el comando a correr para verificar si funciona es
auspice.js --help
auspice.js --v