Difference between revisions of "Applications/HyPhy"
From HPC
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* HYPHYMP is openMP implementation that could utilise more than 1 processors. | * HYPHYMP is openMP implementation that could utilise more than 1 processors. | ||
* HYPHYMPI is MPI implementation that could run on single or multiple nodes. | * HYPHYMPI is MPI implementation that could run on single or multiple nodes. | ||
+ | you can use the openmp version in side an interactive session to define your input arrguments that you can run later as batch job below | ||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@c001 ~]$ interactive | ||
+ | [username@c001 ~]$ HYPHYMP | ||
+ | </pre> | ||
===Batch Script=== | ===Batch Script=== |
Revision as of 14:47, 26 March 2018
Application Details
- Description: HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning
- Version: 2.2.7
- Module: hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
- Licence: Open source
Usage Examples
Currently its available only after through interactive session. its not possible to run it on login nodes of Viper
Module
[username@c001 ~]$ module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
or
[username@c001 ~]$ module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
Description
There are two binaries available.
- HYPHYMP is openMP implementation that could utilise more than 1 processors.
- HYPHYMPI is MPI implementation that could run on single or multiple nodes.
you can use the openmp version in side an interactive session to define your input arrguments that you can run later as batch job below
[username@c001 ~]$ interactive [username@c001 ~]$ HYPHYMP
Batch Script
#!/bin/bash #SBATCH -J amphibio_meme # Job Name #SBATCH -N 1 # Number of Nodes to use #SBATCH -n 28 # Number of CPUs #SBATCH -o %N.%j.%a.out # Output file name #SBATCH -e %N.%j.%a.err # Error file name #SBATCH -p compute # Partition to run on #SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM) module load hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2 (echo "10"; echo "4"; echo "2"; echo "/pass/to/input1/example.fas"; echo "/pass/to/input2/example.tre"; echo "1"; echo "d") | HYPHYMP