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To adapt recount-pump to a new HPC system:

  • Make a subdirectory
  • Install miniconda and some python packages:
(install miniconda)
conda config --add channels conda-forge
conda install watchtower docopt pytest psutil sqlalchemy psycopg2 awscli
  • Install globus_sdk python module, which is only available via pip:
pip install globus_sdk
  • You'll need your ~./aws/credentials file populated for any AWS profiles you refer to in the configs
  • Thins you may need to add to your bash profile:
    • Adding conda to the PATH
    • module load singularity
    • Set SINGULARITY_CACHEDIR
  • In projects/common/clusters/stampede2

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Cluster config files for recount-pump

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