Update memory parameter for megahit to be 80% instead of 20%

dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.

https://dahak-metagenomics.github.io/dahak

BSD 3-Clause "New" or "Revised" License

21 stars 4 forks source link

Update memory parameter for megahit to be 80% instead of 20% #115

Closed ctb closed 6 years ago

ctb commented 6 years ago

Merge Checklist

[x] Typos are a sign of poorly maintained code. Has this request been checked with a spell checker?
[x] Tutorials should be universally reproducible. If this request modifies a tutorial, does it assume we're starting from a blank Ubuntu 16.04 (Xenial Xerus) image?
[x] Large diffs to binary or data files can artificially inflate the size of the repository. Are there large diffs to binary or data files, and are these changes necessary?

ctb commented 6 years ago

Not sure if we want to merge this, but it does fix problems on low memory machines. I think better approach might make this to make memory a default parameter that can be overridden.

charlesreid1 commented 6 years ago

See PR #118 which implements a generic fix for specifying memory usage for both assemblers

charlesreid1 commented 6 years ago

Addressed by #118 (merged into snakemake-comparison)