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The usage is:
module load anaconda/4.00py2.7
OR:
module load anaconda/4.00py3.5
Manual Usage:
You will need to activaterun thethis environment.after Forloading example,the tomodules:
activate biopython
source activate biopython
discarding /sw/anaconda/2.0.1/bin from PATH
prependingsource /sw/anaconda/py27-ver400/etc/profile.d/conda.sh #if using module load anaconda/4.00py2.7
OR source /sw/anaconda/2.0.1/envs/biopython/bin to PATH
To deactivate this environment, use:
source deactivate
Module Usage:
=============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,You to canactivate usebiopython
this
tosource loadactivate 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 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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conda create -n biopython biopython
Fetching package metadata: ..
Solving package specifications: .
Package plan for installation in environment /sw/anaconda/2.0.1/envs/biopython:
The following packages will be downloaded:
package | build
---------------------------|-----------------
biopython-1.64 | np18py27_0 2.1 MB
python-2.7.8 | 0 11.3 MB
------------------------------------------------------------
Total: 13.5 MB
The following packages will be linked:
package | build
---------------------------|-----------------
biopython-1.64 | np18py27_0 hard-link
numpy-1.8.1 | py27_0 hard-link
openssl-1.0.1h | 0 hard-link
python-2.7.8 | 0 hard-link
readline-6.2 | 2 hard-link
sqlite-3.8.4.1 | 0 hard-link
system-5.8 | 1 hard-link
tk-8.5.15 | 0 hard-link
zlib-1.2.7 | 0 hard-link
Proceed ([y]/n)? y
Fetching packages ...
biopython-1.64 100% |##########################| Time: 0:00:15 144.95 kB/s
python-2.7.8-0 100% |##########################| Time: 0:00:14 821.86 kB/s
Extracting packages ...
[ COMPLETE ] |#######################| 100%
Linking packages ...
[ COMPLETE ] |#######################| 100%
#
# To activate this environment, use:
# $ source activate biopython
#
# To deactivate this environment, use:
# $ source deactivate
#
|
Installed Environment
use:
# $ source deactivate
#
|
Installed Environment
Useful commands
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Useful commands:
conda info --envs
conda list
conda activate |
Sample PBS file
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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
module load anaconda/4.00py2.7
source /sw/anaconda/py27-ver400/etc/profile.d/conda.sh
##use /sw/anaconda/py3-ver400/etc/profile.d/conda.sh if using “module load anaconda/4.00py3.5”
echo "Starting job: "
cd $PBS_O_WORKDIR
python <pythonFile>
>>>An example of the python file>>>>>>>>>
cat pythonFile.py
import tensorflow as tf
>>>>>>>>>>>>>>
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Activate an environment
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source /sw/anaconda/py27-ver400/etc/profile.d/conda.sh
OR source /sw/anaconda/py3-ver400/etc/profile.d/conda.sh if using “module load module load anaconda/4.00py3.5”
source activate biopython
e.g:
source activate biopython
discarding /sw/anaconda/2.0.1/bin from PATH
prepending /sw/anaconda/2.0.1/envs/biopython/bin to PATH
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1. http://davebehnke.com/using-python-anaconda-distribution.html
2. https://store.continuum.io/cshop/anaconda/
3. http://continuum.io/downloads#all