Difference between revisions of "Applications/HyPhy"
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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. | ||
| + | |||
| + | ===Batch Script=== | ||
| + | |||
| + | |||
| + | <pre style="background-color: #C8C8C8; color: black; border: 2px solid #C8C8C8; font-family: monospace, sans-serif;"> | ||
| + | |||
| + | #!/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 | ||
| + | </pre> | ||
Revision as of 14:44, 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.
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