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Name: A Vathrakokoili-Pournara

Type: User

Company: EMBL-EBI

Bio: PhD fellow @Papatheodorou-Group at EMBL-EBI and Cambridge University Interested in developing tools to understand composition in cancer tissues.

Twitter: AnnaVathrakoko1

Location: Cambridge

CODON MIGRATION

login

ssh codon-login # use your credentials

set up your .bashrc and .bash_profile under /homes/YOURUSERNAME

Where to store data, where to work in codon

store important permanent data under /nfs/research/irene/YOURUSERNAME

run jobs, store intermediate outputs that you dont need for long term here : /hps/nobackup/irene/ma/YOURUSERNAME

cd /hps/nobackup/irene/ma
mkdir YOURUSERNAME

install software, conda env etc here : /hps/software/users/ma/YOURUSERNAME

cd /hps/software/users/ma/
mkdir YOURUSERNAME

How to move data from yoda to codon

navigate in codon:

cd /nfs/research/irene/YOURUSERNAME

RUN DATA MOVING JOB

bsub -n 8 -q datamover "/hps/software/copytools/msrsync/msrsync -p 8 /nfs/yoda/leia/research/ma/YOURUSERNAME /nfs/research/irene/

#the above command will use 8 cores, the datamover queue and it will move the whole directory YOURUSERNAME from yoda to codon.

CONDA

install minicinda instead of Annaconda (bacause it is lighter) in codon

Follow the instructions here : To install conda download the installer script from https://docs.conda.io/en/latest/miniconda.html and follow the instructions https://conda.io/projects/conda/en/latest/user-guide/install/linux.html

install miniconda under : /hps/software/users/ma/YOURUSERNAME
Once miniconda is installed in codon go to yoda

export environments from yoda

conda info --envs # prints the environments you have on yoda- select which ones you use and you want to move to codon

EXAMPLE: export the base environment

mkdir yml_files
conda activate base
bsub -M 1200 -n 4 conda env export > yml_files/base.yml
conda deactivate

Repeat the above 3 steps to export all the environments in yml files.

move the yml files to codon

bsub -n 8 -q datamover "/hps/software/copytools/msrsync/msrsync -p 8 /nfs/yoda/leia/research/ma/YOURUSERNAME/yml_files /hps/software/users/ma/YOURUSERNAME/

build environments from yml files

cd /hps/software/users/ma/YOURUSERNAME/
conda env create -f yml_files/base.yml

check your environment

conda activate base
conda list

repeat for the other environments

A Vathrakokoili-Pournara 's Projects