guppy-software
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guppy-software [2021/07/08 08:10] – created aorth | guppy-software [2023/12/06 06:42] (current) – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: | + | * Version: |
* Added: July, 2021 | * Added: July, 2021 | ||
- | * Models: / | + | * Updated: December, 2023 |
- | * Link: https:// | + | |
===== Usage ===== | ===== Usage ===== | ||
+ | Guppy is only available on compute06 because this is the only node that has a GPU. | ||
- | See versions of guppy that are available: | + | // |
- | < | + | ===== Installation ====== |
- | Load one version into your environment and run it: | ||
- | < | ||
- | |||
- | **Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult: / | ||
- | |||
- | ===== Installation ====== | ||
Notes from the sysadmin during installation. | Notes from the sysadmin during installation. | ||
- | < | + | < |
- | $ wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_5.0.11_linux64.tar.gz | + | |
- | $ tar xf ont-guppy_5.0.11_linux64.tar.gz | + | |
- | $ sudo mkdir -p / | + | |
- | $ sudo cp -r ont-guppy / | + | |
Run some test data using fourteen CPUs: | Run some test data using fourteen CPUs: | ||
- | < | + | < |
- | $ mkdir -p / | + | $ cd / |
$ wget https:// | $ wget https:// | ||
- | $ tar xf Data_Group1.tar.gz | + | $ tar xf Data_Group1.tar.gz |
- | $ guppy_basecaller --compress_fastq -i / | + | $ guppy_basecaller --compress_fastq -i data/ |
... | ... | ||
- | Caller time: 208271 | + | Caller time: 3281435 |
Run some test data using a GPU (currently only on compute06): | Run some test data using a GPU (currently only on compute06): | ||
- | < | + | < |
+ | $ guppy_basecaller --device " | ||
... | ... | ||
- | Caller time: 2994 ms, Samples called: 27619692, samples/ | + | Caller time: 4366 ms, Samples called: 27619692, samples/ |
guppy-software.txt · Last modified: 2023/12/06 06:42 by aorth