Add option to use remote or local guppy GPU basecalling - Githubissues

JensUweUlrich / ReadBouncer

Fast and scalable nanopore adaptive sampling

GNU General Public License v3.0

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Add option to use remote or local guppy GPU basecalling #23

Closed JensUweUlrich closed 2 years ago

JensUweUlrich commented 2 years ago

Users should have the option to decide whether to use local CPU base calling with DeepNano or local/remote GPU base calling with Guppy.

Tasks:

Add option to the TOML configuration

[Basecaller]
caller= DeepNano/Guppy
remote_host=xxx.xxx.xxx.xxx
remote_port=xx

divide libBasecaller into two subprojects and add ZeroMQ to the CMake project for Guppy base calling
create structs, objects and methods for message exchange with basecall_server

JensUweUlrich commented 2 years ago

Guppy basecalling merged to master; TOML integration is part of bug #22