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The usage is:
module load anaconda3/2019.07.py3
OR
module load anaconda/4.00py2.7
OR:
module load anaconda/4.00py3.5
You need to run this after loading the modules:
source /sw/anaconda/py27-ver400/etc/profile.d/conda.sh #if using module load anaconda/4.00py2.7
OR source /sw/anaconda/py3-ver400/etc/profile.d/conda.sh #if using “module load anaconda/4.00py3.5”
Manual Usage:
You will need to activate the environment. For example, to activate biopython
source activate biopython
discarding /sw/anaconda/2.0.1/bin from PATH
prepending /sw/anaconda/2.0.1/envs/biopython/bin to PATH
To deactivate this environment, use:
source deactivate
Module Usage:
=============
For example,You can use this to load biopython using python 2.7 version (anaconda) :
module load anaconda/py27biopython1.66
For python 3.5 (anaconda env), use this:
module load anaconda/py35biopython1.66
Anaconda environment need not be loaded separately.
However, it can be loaded as follows if needed for other reasons:
module load anaconda/4.00py2.7
module load anaconda/4.00py3.5
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#!/bin/bash
#PBS -N condatest
#PBS -m abe
#PBS -M YourEMAIL@griffith.edu.au
#PBS -l select=1:ncpus=1:mem=4gb,walltime=10:00:00
cd $PBS_O_WORKDIR
module load anaconda3/2019.07py3
source activate bioinformatics
trinity <trinityinput>
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Sample python code to write out a plot
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vi plot.py >>>>>>>>>>>>>>>>> import matplotlib.pyplot as plt import numpy as np np.random.seed(19680801) data = np.random.randn(2, 100) fig, axs = plt.subplots(2, 2, figsize=(5, 5)) axs[0, 0].hist(data[0]) axs[1, 0].scatter(data[0], data[1]) axs[0, 1].plot(data[0], data[1]) axs[1, 1].hist2d(data[0], data[1]) plt.show() plt.savefig('test') >>>>>>>>>>>>>>>>>> module load anaconda3/2022.10 source activate yourenv #this should have the matlibplot packages and others. python plot.py would generate a plot named test.png Reference: https://matplotlib.org/3.4.3/tutorials/introductory/sample_plots.html Sample codes are here: https://matplotlib.org/3.4.3/_downloads/55a714c8a6e4dde456b09326202fe492/sample_plots.py https://matplotlib.org/3.4.3/_downloads/003118d8eb1e7df55671bcdf18bfac3c/sample_plots.ipynb |
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