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guppy-software [2022/07/07 11:14] aorthguppy-software [2023/12/06 06:42] (current) aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 6.0.1+  * Version: 6.5.7
   * Added: July, 2021   * Added: July, 2021
-  * Updated: May2022 +  * Updated: December2023
-  * Models: /export/apps/guppy/6.0.1/data +
-  * Link: https://community.nanoporetech.com/downloads/guppy/release_notes +
-  * Version check: https://hub.docker.com/r/genomicpariscentre/guppy-gpu/tags+
  
 ===== Usage ===== ===== Usage =====
 +Guppy is only available on compute06 because this is the only node that has a GPU.
  
-See versions that are available: +//Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult/opt/ont/guppy/data.// 
-<code>$ module avail guppy</code>+===== Installation ======
  
-Load one version into your environment and run it: 
-<code>$ module load guppy/6.0.1</code> 
- 
-//Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult: /export/apps/guppy/6.0.1/data. 
-// 
-===== Installation ====== 
 Notes from the sysadmin during installation. Notes from the sysadmin during installation.
  
-<code>cd /tmp +<code>sudo dnf install https://hpc.ilri.cgiar.org/~jbaka/ONT-Dec2023/Software/ont-guppy-6.5.7-1.el8.x86_64.rpm</code>
-$ wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_6.0.1_linux64.tar.gz +
-$ sudo cp -r ont-guppy /export/apps/guppy/6.0.1</code>+
  
 Run some test data using fourteen CPUs: Run some test data using fourteen CPUs:
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 Run some test data using a GPU (currently only on compute06): Run some test data using a GPU (currently only on compute06):
  
-<code>$ module load guppy/6.0.1 +<code>$ srun --gres=gpu:v100:1 --partition=batch -w compute06 -n 1 -J guppy --pty bash
-$ srun --gres=gpu:v100:1 --partition=batch -w compute06 -n 1 -J guppy --pty bash+
 $ guppy_basecaller --device "cuda:0" --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg $ guppy_basecaller --device "cuda:0" --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg
 ... ...
 Caller time: 4366 ms, Samples called: 27619692, samples/s: 6.32609e+06</code> Caller time: 4366 ms, Samples called: 27619692, samples/s: 6.32609e+06</code>
guppy-software.1657192488.txt.gz · Last modified: 2022/07/07 11:14 by aorth