cgatpipelines_on_new_cluster.md

Installing cgat pipeline code on new cluster

1. Export conda envirnoment.yml file from old cluster using conda --no-build

2. On new cluster - download miniconda3 in home -> follow workshop - reset channels so conda-forge is at top

3. Install mamba in base enviroment

4. create env from yml file using mamba

5. when source conda there is an issue with the system conda interfering

   • use sed to remove it from the path before source
   • then source conda
   • conda activate base
   • conda deactivate # otherwise will not prepend path correctly when change env

   test by doing which python in different environments

   • conda activate base

   • conda activate environment_new (check python path - should now be ok)

   • need to put conda activate in if PS1 so that conda env will be inherited correctly when running pipelines

6)installing cgatcode

• install cgatapps via conda mamba install to get all dependencies

• mamba remove --force cgatapps (just removes cgatapps)

• update cython conda install cython=0.29 to install cgatapps repo

• download cgatapps repo

• python setup.py develop

• download cgatflow

• python setup.py develop

• installed juptyer lab

• installed dataclasses