To get a list of environment in anaconda:
conda info -e
To create an environment:
conda create -n biopython biopython


De-Activate an environment

source deactivate



Deleting an environment

conda remove -n biopython

conda create -h
usage: conda create [-h] [--yes] [--dry-run] [-f] [--file FILE] [--unknown]
               package versions to install into conda environment

optional arguments:
  -h, --help [--no-deps] [-m] [--use-index-cache] [--use-local]
            show this help message and exit   [--yes   no-pin] [-c CHANNEL] [--override-channels]
             do not ask for confirmation   [--dry-runn NAME | -p PATH]         only display what would have been done
  -f, --force [-q] [--alt-hint] [--clone ENV]
         force install (even when package already installed),     [--no-default-packages]
                   implies --no-deps
  --file FILE           read package versions from FILE
  --unknown             use index metadata from the local package cache (which
   [package_spec [package_spec ...]]

Create a new conda environment from a list of specified packages. To use the created environment, use 'source activate envname' look in that directory first.  This command requires either the -n NAME or -p PREFIX option.

positional arguments:
  package_spec          package versions to install into conda environment

optional arguments:
  are from unknown channels)-h, --help      --no-deps      show this help message and exit
 do not--yes install dependencies   -m, --mkdir           createdo prefixnot directoryask iffor necessaryconfirmation
  --usedry-index-cacherun     use cache of channel index files   --use-local     only display what would have been done
  -f, --force  use locally built packages   --no-pin   force install (even when package already installed),
    don't use pinned packages   -c CHANNEL, --channel CHANNEL           implies --no-deps
  --file FILE         additional channel toread searchpackage forversions packages.from TheseFILE
are  --unknown             use index metadata from the local package cache (which
 URLs searched in the order they are given (including               are from unknown channels)
  --no-deps    file:// for local directories). Then, the defaults or  do not install dependencies
  -m, --mkdir           create prefix directory if necessary
  channels from .condarc are searched (unless
       --use-index-cache     use cache of channel index files
  --use-local           use locally built packages
  --overrideno-channelspin is given). You can use 'defaults'        don't use pinned packages
  -c CHANNEL, --channel CHANNEL
       to get the default packages for conda, and 'system' to        additional channel to search for packages. These are
          get   the system packages, which also takes .condarc     URLs searched in the order they are given (including
           into account. You can also use any name and the    file:// for local directories). Then, the defaults or
             .condarc channel_alias value will be prepended. The     channels from .condarc are searched (unless
              default channel_alias is http://conda.binstar.org/        --override-channels is given). DoYou notcan searchuse default'defaults'
or .condarc channels. Requires                     to get the default --channel.packages for  -n NAMEconda, --name NAME  name of environment (in /sw/anaconda/2.0.1/envs)
  -p PATH, --prefix PATHand 'system' to
                        get the system packages, which also takes .condarc
   full path to environment prefix (default:                into account. You can also use any name  /sw/anaconda/2.0.1)and the
  -q, --quiet           do not display progress bar   --alt-hint   .condarc channel_alias value will be prepended. The
  Use an alternate algorithm to generate an                default channel_alias is http://conda.binstar.org/
  --override-channels   unsatisfiable hintDo not search default or .condarc channels. Requires
  --clone ENV           path to (or name of) existing local environment   --no-default-packageschannel.
  -n NAME, --name NAME  name of environment (in /sw/anaconda/2.0.1/envs)
  -p PATH, --prefix PATH
       ignore create_default_packages in condarc file  examples:     conda create -n myenv sqlite  

bash Anaconda-2.0.1-Linux-x86_64.sh

Anaconda will now be installed into this location:
/root/anaconda

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify an different location below

[/root/anaconda] >>> /sw/anaconda/2.0.1

PREFIX=/sw/anaconda/2.0.1
installing: python-2.7.7-0 ...
installing: itsdangerousconda-03.5.245-py27_0 ...
installing: jdcalconda-build-1.03.5-py27_0 ...
installing: jinja2_license-21.7.21-py27_0 ...
installing: jpeg-8d-argcomplete-0.6.7-py27_0 ...
installing: kiwisolverastropy-0.13.2-py27np18py27_0 ...
installing: launcheratom-0.13.57-py27_0 ...
installing: lcms-1.19-beautiful-soup-4.3.1-py27_0 ...
installing: libdyndbinstar-0.65.23-py27_0 ...
installing: libpngbitarray-10.58.131-1py27_0 ...
installing: libsodiumblaze-0.45.50-0np18py27_1 ...
installing: libtiffblz-40.06.2-np18py27_0 ...
installing: libxml2bokeh-20.94.04-0np18py27_1 ...
installing: libxsltboto-12.128.280-py27_0 ...
installing: llvmcairo-31.12.32-02 ...
installing: llvmpycasuarius-01.12.61-py27_0 ...
installing: lxmlcdecimal-32.3.5-py27_0 ...
installing: markupsafechaco-04.4.181-py27np18py27_0 ...
installing: matplotlibcolorama-10.32.17-np18py27py27_10 ...
installing: mockconfigobj-15.0.15-py27_0 ...
installing: mpi4pycubes-10.10.32-py27_04 ...
installing: mpich2curl-17.430.1p10-0 ...
installing: multipledispatchcython-0.420.31-py27_0 ...
installing: networkxdatashape-10.82.10-py27np18py27_01 ...
installing: nltkdateutil-2.0.41-np18py27py27_02 ...
installing: nosedocutils-10.3.311-py27_0 ...
installing: numbadynd-python-0.136.2-np18py27_0 ...
installing: numexprenable-24.3.10-np18py27_02 ...
installing: numpyenaml-10.89.1-py27_01 ...
installing: openpyxlflask-10.810.51-py27_01 ...
installing: opensslfreetype-12.04.1h10-0 ...
installing: pandasfuture-0.1412.01-np18py27py27_0 ...
installing: patsygevent-1.0.2.1-np18py27py27_0 ...
installing: pep8gevent-1websocket-0.59.63-py27_0 ...
installing: pilgreenlet-10.14.72-py27_10 ...
installing: pipgrin-1.52.61-py27_01 ...
installing: pixmanh5py-02.263.20-np18py27_0 ...
installing: plyhdf5-31.8.49-py27_01 ...
installing: psutilipython-2.1.10-py27_02 ...
installing: pyipython-notebook-2.1.4.200-py27_0 ...
installing: py2cairoipython-qtconsole-2.1.10.0-py27_10 ...
installing: pycosatitsdangerous-0.6.124-py27_0 ...
installing: pycparserjdcal-21.100-py27_0 ...
installing: pycryptojinja2-2.67.12-py27_0 ...
installing: pycurl-7.19.3.1-py27_2jpeg-8d-0 ...
installing: pyfacekiwisolver-40.41.02-py27_0 ...
installing: pyflakeslauncher-0.81.15-py27_0 ...
installing: pygmentslcms-1.619-py27_0 ...
installing: pyparsinglibdynd-20.06.12-py27_0 ...
installing: pyqtlibpng-41.105.413-py27_01 ...
installing: pytableslibsodium-30.14.15-np18py27_0 ...
installing: pytestlibtiff-24.50.2-py27_0 ...
installing: pytzlibxml2-20142.9.30-py27_0 ...
installing: pyyamllibxslt-31.111.28-py27_0 ...
installing: pyzmqllvm-143.3-0 ...
installing: llvmpy-0.12.6-py27_0 ...
installing: qtlxml-43.83.5-py27_0 ...
installing: readlinemarkupsafe-60.218-2py27_0 ...
installing: redismatplotlib-21.63.91-0np18py27_1 ...
installing: redismock-py-21.90.1-py27_0 ...
installing: requestsmpi4py-21.3.0-py27_0 ...
installing: ropempich2-01.94.41p1-py27_10 ...
installing: runipymultipledispatch-0.14.03-py27_0 ...
installing: scikitnetworkx-image-01.108.01-np18py27py27_0 ...
installing: scikitnltk-learn-2.0.14.14-np18py27_10 ...
installing: scipynose-01.143.03-np18py27py27_0 ...
installing: setuptoolsnumba-30.13.62-py27np18py27_0 ...
installing: sipnumexpr-42.153.51-py27np18py27_0 ...
installing: sixnumpy-1.68.1-py27_0 ...
installing: sphinxopenpyxl-1.28.25-py27_0 ...
installing: spyderopenssl-21.30.0rc11h-py27_0 ...
installing: spyderpandas-app-20.314.0rc10-py27np18py27_0 ...
installing: sqlalchemypatsy-0.92.41-py27np18py27_0 ...
installing: sqlitepep8-31.85.4.16-py27_0 ...
installing: ssl_match_hostname-3.4.0.2pil-1.1.7-py27_01 ...
installing: statsmodelspip-01.5.06-np18py27py27_0 ...
installing: sympypixman-0.726.52-py27_0 ...
installing: systemply-53.84-1py27_0 ...
installing: theanopsutil-02.61.01-np18py27py27_0 ...
installing: tkpy-81.54.1520-py27_0 ...
installing: tornadopy2cairo-31.210.10-py27_01 ...
installing: traitspycosat-40.46.01-py27_0 ...
installing: traitsuipycparser-42.4.010-py27_0 ...
installing: ujsonpycrypto-2.6.1.33-py27_0 ...
installing: util-linux-2.21-0pycurl-7.19.3.1-py27_2 ...
installing: werkzeugpyface-04.94.60-py27_0 ...
installing: xlrdpyflakes-0.98.31-py27_0 ...
installing: xlsxwriterpygments-01.5.56-py27_0 ...
installing: xlwtpyparsing-2.0.7.51-py27_0 ...
installing: yamlpyqt-04.110.4-py27_0 ...
installing: zeromqpytables-43.01.41-np18py27_0 ...
installing: zlibpytest-12.25.72-py27_0 ...
installing: anacondapytz-22014.3-py27_0.1-np18py27 ...
installing: pyyaml-3.11-py27_0 ...
installing: _cache-0pyzmq-14.3.0-x0py27_0 ...
Python 2.7.7 :: Continuum Analytics, Inc.
creating default environment...
installation finished.
Do you wish the installer to prepend the Anaconda install location
to PATH in your /root/.bashrc ? [yes|no]
[no] >>> No

Thank you for installing Anaconda!

To see what packages will be downloaded and/or used in an environment before creating it, you can use the --dry-run option.
conda create --dry-run -n foo2 python

e.g.:

conda create --dry-run -n biopython biopython
Fetching package metadata: ..
Solving package specifications: .
Package plan for installation in environment /sw/anaconda/2.0.1/envs/biopython1.64:

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

Dry run: exiting

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 downloadedlinked:

    package                    |            build
    ---------------------------|-----------------
    biopython-1.64             |       np18py27_0   hard-link
    numpy---1.8.1                |           py27_0   hard-link
    biopythonopenssl-1.0.641h             |         np18py27_0       0  2.1 MB hard-link
    python-2.7.8               |                0   hard-link
    11.3 MB
    ------------------------------------------------------------readline-6.2               |                2   hard-link
    sqlite-3.8.4.1        Total:      |       13.5 MB  The following packages will be linked: 0   hard-link
 package   system-5.8                 |            build      ---------------------------|-----------------1   hard-link
    biopythontk-1.648.5.15                  |       np18py27_         0   hard-link
    numpyzlib-1.82.17                 |            py27_    0   hard-link

Proceed ([y]/n)? y
 opensslFetching packages ...
biopython-1.0.1h64 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      0] |#######################| 100%
hard-linkLinking     python-2.7.8 packages ...
[      COMPLETE      ]  |#######################| 100%
#
# To activate this environment, use:
# $ source activate biopython
#
# 0To deactivate this hard-link
    readline-6.2               |                2   hard-link
    sqlite-3.8.4.1             |                0   hard-link
    system-5.8                 |                1   hard-link
    tk-8.5.15environment, use:
# $ source deactivate
#

Useful commands:
 
conda info --envs
conda list
conda activate

#!/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
>>>>>>>>>>>>>> 

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

source deactivate

conda remove -n biopython

module load anaconda/5.3.1py3

conda info --envs
# conda environments:
#
base                  |*    /sw/centos7/anaconda/5.3.1/py3
accelerate            0   hard-link
    zlib-1.2.7 /sw/centos7/anaconda/5.3.1/py3/envs/accelerate
biopython                | /sw/centos7/anaconda/5.3.1/py3/envs/biopython
deeplearning               0   hard-link

Dry run: exiting

Instructions from: https://medium.com/@danielwzou/installing-spacy-and-other-packages-without-sudo-or-root-privileges-using-anaconda-59571ec0ecad

First, navigate to your home directory.
module load anaconda/5.3.1py3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
Now, we have a local installation of the Conda package manager at ~/miniconda3
Let’s add conda to our bash profile so that we can call it from the command line
vim .bash_profile
i
Add this line to the file:
export PATH=$HOME/miniconda3/bin:$PATH
esc :wq
Now, let’s reload our .bash_profile
source .bash_profile
And check that our installation was completed successfully
which conda
Which should return ~/miniconda3/bin/conda
Now that Conda is installed, we can install Spacy or other Python packages
conda install spacy
python -m spacy download en
Now, let’s make sure that Spacy is installed correctly
python
import spacy
nlp = spacy.load('en')
doc = nlp(u'Hello World!')
print([w.lemma_ for w in doc])
Now that you have Conda installed, you can use it to install many packages locally.

module load anaconda3/2019.07py3
 
This should have packages like the tensorflow env. You can find with this:
conda info --envs
 
>>>>> 
conda info --envs
# conda environments:
#
                           |/sw/anaconda2/2019.07/envs/bio
            build     ---------------------------|-----------------        biopython-1.64/sw/anaconda2/2019.07/envs/bioinfoPy27
base                  *  /sw/anaconda3/2019.07
3point6   |       np18py27_0   hard-link     numpy-1.8.1/sw/anaconda3/2019.07/envs/3point6
R                        | /sw/anaconda3/2019.07/envs/R
bioinformatics          py27_0   hard-link
    openssl-1.0.1h             |                0   hard-link
    python-2.7.8 /sw/anaconda3/2019.07/envs/bioinformatics
 
>>>>>>> 
This will give the packages in the base:
conda list
 
source activate 3point6
Next run: " conda list"
This will list the packages installed in that environment.
 
It shows among many others:
pytorch                |   1.3.1           cuda100py36h53c1284_0
 0
tensorboard  hard-link     readline-6.2        2.0.0       |       pyhb230dea_0
tensorflow        2   hard-link     sqlite-32.80.4.10           mkl_py36hef7ec59_0
tensorflow-base |          2.0.0      0   hard-link  mkl_py36h9204916_0
tensorflow-estimator  system-5.8    2.0.0             | pyh2649769_0
termcolor              1   hard-link1.1.0     tk-8.5.15                  py_2 |   conda-forge
theano            0   hard-link     zlib-1.2.70.4           py36hf484d3e_1000    conda-forge
 
Remember this cluster has no GPU (currently)

#!/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  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
#

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