snakemake, singularity, and HPC

Posted on Mon 01 August 2022 in posts • Tagged with hpc, python, reproducibility

This is a bit of a sequel to my post last May about using conda environments with snakemake on the HPC. That solution worked for me, but was hacky and limited. This post will describe a different solution, which uses a singularity container containing a conda environment that can be …

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conda, snakemake, and HPC

Posted on Wed 05 May 2021 in posts • Tagged with hpc

NOTE: I have since come up with a solution that I like better / think is less hacky, described in this post.

NYU's new high performance computing (HPC) cluster, Greene, was put into production earlier this year and, on the new system, they want all users to use singularity containers for …

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