# Getting custom conda environment loaded into ARE environment

**URL:** <https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499>\
**Category:** Infrastructure\
**Tags:** are\
**Created:** [12 May 2025 09:38 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499 "2025-05-12T09:38:05Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\
**Post date:** [12 May 2025 09:38 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/1 "2025-05-12T09:38:05Z")

</div>

Evening all.

The World Climate Research Program 2025 Hackathon is trying to build a temporary python environment to get around the current disk issues on gadi.

We want to build a python environment on `/scratch/nf33` which can then be used in ARE sessions.

The .`yaml` file is available from [tools/python\_envs/environment.yaml at main · digital-earths-global-hackathon/tools · GitHub](https://github.com/digital-earths-global-hackathon/tools/blob/main/python_envs/environment.yaml)

So I downloaded and installed miniconda (because I can’t rely on existing `hh5/xp65 /g/data` conda installs) at this location  
`/scratch/nf33/public/miniconda `  
and ran

```auto
conda env create --name digital_earths_env --file environment.yaml

```

Which created an environment in  
`/scratch/nf33/public/miniconda/envs/digital_earths_env`  
This environment can be activated from the command line and the requisite modules imported.

Now, the trick part to loading it into ARE.

The NRI ARE docs state:  
“ **Python or Conda virtual environment base**  
Path to a Python or conda base environment to be activated for the JupyterLab session.  
It is the equivalent to running `source <path/to/environment/bin/activate>` on the command line.”

The problem is, this `<environment>/bin/activate` file doesn’t exist. So my ARE sessions can’t find any kernels associated with the environment.

This is a known issue with new conda, see

> <https://github.com/conda/conda/issues/6983>
>
> \*\*I'm submitting a...\*\*
> - \[X\] bug report
> - \[\] feature request
> 
> 
> \## Cur…rent Behavior
> 
> \`conda create\` no longer creates a symlink to \`$\_CONDA\_ROOT/bin/activate\` for the new environment.
> 
> It seems to have been some changes to activation in \`conda\` which may be the reason for this. Causes jorgenschaefer/pyvenv#67
> 
> \### Steps to Reproduce
> 
> \`\`\`
> conda create -n venv python==3.6
> ls $\_CONDA\_ROOT/envs/venv/bin/activate
> \`\`\`
> Output
> \`\`\`
> ls: cannot access '/home/kevin/anaconda/envs/venv/bin/activate': No such file or directory
> \`\`\`
> 
> \## Expected Behavior
> 
> A symlink to \`$\_CONDA\_ROOT/bin/activate\` to be created
> 
> \## Environment Information
> \<details open\>\<summary\>\<code\>\`conda info\`\</code\>\</summary\>\<p\>
> 
> 
> \`\`\`
> active environment : None
> shell level : 0
> user config file : /home/kevin/.condarc
> populated config files : 
> conda version : 4.4.10
> conda-build version : 3.0.23
> python version : 3.6.2.final.0
> base environment : /home/kevin/anaconda (writable)
> channel URLs : https://repo.continuum.io/pkgs/main/linux-64
> https://repo.continuum.io/pkgs/main/noarch
> https://repo.continuum.io/pkgs/free/linux-64
> https://repo.continuum.io/pkgs/free/noarch
> https://repo.continuum.io/pkgs/r/linux-64
> https://repo.continuum.io/pkgs/r/noarch
> https://repo.continuum.io/pkgs/pro/linux-64
> https://repo.continuum.io/pkgs/pro/noarch
> package cache : /home/kevin/anaconda/pkgs
> /home/kevin/.conda/pkgs
> envs directories : /home/kevin/anaconda/envs
> /home/kevin/.conda/envs
> platform : linux-64
> user-agent : conda/4.4.10 requests/2.18.4 CPython/3.6.2 Linux/4.15.6-1-ARCH arch/ glibc/2.26
> UID:GID : 1000:1000
> netrc file : /home/kevin/.netrc
> offline mode : False
> \`\`\`
> \</p\>\</details\>
> 
> 
> \<details open\>\<summary\>\<code\>\`conda config --show-sources\`\</code\>\</summary\>\<p\>
> 
> 
> Nothing is returned
> \`\`\`
> 
> \`\`\`
> \</p\>\</details\>
> 
> 
> \<details\>\<summary\>\<code\>\`conda list --show-channel-urls\`\</code\>\</summary\>\<p\>
> 
> 
> \`\`\`
> \# packages in environment at /home/kevin/anaconda:
> \#
> \# Name Version Build Channel
> \_ipyw\_jlab\_nb\_ext\_conf 0.1.0 py36he11e457\_0 defaults
> \_nb\_ext\_conf 0.4.0 py36\_1 defaults
> airflow 1.8.0 \<pip\>
> alabaster 0.7.10 py36h306e16b\_0 defaults
> alembic 0.8.10 \<pip\>
> anaconda custom py36hbbc8b67\_0 defaults
> anaconda-client 1.6.5 py36h19c0dcd\_0 defaults
> anaconda-navigator 1.6.8 py36h672ccc7\_0 defaults
> anaconda-project 0.8.0 py36h29abdf5\_0 defaults
> asn1crypto 0.22.0 py36h265ca7c\_1 defaults
> astroid 1.5.3 py36hbdb9df2\_0 defaults
> astropy 2.0.2 py36ha51211e\_4 defaults
> babel 2.5.0 py36h7d14adf\_0 defaults
> backports 1.0 py36hfa02d7e\_1 defaults
> backports.shutil\_get\_terminal\_size 1.0.0 py36hfea85ff\_2 defaults
> basemap 1.0.7 np113py36\_0 defaults
> beautifulsoup4 4.6.0 py36h49b8c8c\_1 defaults
> bitarray 0.8.1 py36h5834eb8\_0 defaults
> bkcharts 0.2 py36h735825a\_0 defaults
> blaze 0.11.3 py36h4e06776\_0 defaults
> bleach 2.0.0 py36h688b259\_0 defaults
> bokeh 0.12.7 py36h169c5fd\_1 defaults
> boto 2.48.0 py36h6e4cd66\_1 defaults
> bottleneck 1.2.1 py36haac1ea0\_0 defaults
> ca-certificates 2017.08.26 h1d4fec5\_0 defaults
> cairo 1.14.10 h58b644b\_4 defaults
> certifi 2018.1.18 py36\_0 defaults
> cffi 1.10.0 py36had8d393\_1 defaults
> chardet 3.0.4 py36h0f667ec\_1 defaults
> click 6.7 py36h5253387\_0 defaults
> click-plugins 1.0.3 \<pip\>
> cligj 0.4.0 \<pip\>
> cloudpickle 0.4.0 py36h30f8c20\_0 defaults
> clyent 1.2.2 py36h7e57e65\_1 defaults
> colorama 0.3.9 py36h489cec4\_0 defaults
> conda 4.4.10 py36\_0 defaults
> conda-build 3.0.23 py36h1da9bb0\_0 defaults
> conda-env 2.6.0 h36134e3\_1 defaults
> conda-verify 2.0.0 py36h98955d8\_0 defaults
> contextlib2 0.5.5 py36h6c84a62\_0 defaults
> croniter 0.3.19 \<pip\>
> cryptography 2.0.3 py36ha225213\_1 defaults
> curl 7.55.1 hcb0b314\_2 defaults
> cycler 0.10.0 py36h93f1223\_0 defaults
> cython 0.26.1 py36h21c49d0\_0 defaults
> cytoolz 0.8.2 py36h708bfd4\_0 defaults
> dask 0.15.2 py36h9b48dc4\_0 defaults
> dask-core 0.15.2 py36h0f988a8\_0 defaults
> datashape 0.5.4 py36h3ad6b5c\_0 defaults
> dbus 1.10.22 h3b5a359\_0 defaults
> decorator 4.1.2 py36hd076ac8\_0 defaults
> descartes 1.1.0 \<pip\>
> dill 0.2.7.1 \<pip\>
> distributed 1.18.3 py36h73cd4ae\_0 defaults
> docutils 0.14 py36hb0f60f5\_0 defaults
> entrypoints 0.2.3 py36h1aec115\_2 defaults
> et\_xmlfile 1.0.1 py36hd6bccc3\_0 defaults
> expat 2.2.4 hc00ebd1\_1 defaults
> fastcache 1.0.2 py36h5b0c431\_0 defaults
> fastkml 0.11 \<pip\>
> filelock 2.0.12 py36hacfa1f5\_0 defaults
> Fiona 1.7.11 \<pip\>
> flake8 3.5.0 \<pip\>
> flask 0.12.2 py36hb24657c\_0 defaults
> Flask 0.11.1 \<pip\>
> Flask-Admin 1.4.1 \<pip\>
> Flask-Cache 0.13.1 \<pip\>
> flask-cors 3.0.3 py36h2d857d3\_0 defaults
> Flask-Login 0.2.11 \<pip\>
> flask-swagger 0.2.13 \<pip\>
> Flask-WTF 0.12 \<pip\>
> fontconfig 2.12.4 h88586e7\_1 defaults
> freetype 2.8 h52ed37b\_0 defaults
> funcsigs 1.0.0 \<pip\>
> future 0.15.2 \<pip\>
> geojson 2.3.0 \<pip\>
> geopandas 0.3.0 \<pip\>
> geos 3.5.0 0 defaults
> get\_terminal\_size 1.0.0 haa9412d\_0 defaults
> gevent 1.2.2 py36h2fe25dc\_0 defaults
> gitdb2 2.0.3 \<pip\>
> GitPython 2.1.7 \<pip\>
> glib 2.53.6 hc861d11\_1 defaults
> glob2 0.5 py36h2c1b292\_1 defaults
> gmp 6.1.2 hb3b607b\_0 defaults
> gmpy2 2.0.8 py36h55090d7\_1 defaults
> graphite2 1.3.10 hc526e54\_0 defaults
> greenlet 0.4.12 py36h2d503a6\_0 defaults
> gst-plugins-base 1.12.2 he3457e5\_0 defaults
> gstreamer 1.12.2 h4f93127\_0 defaults
> gunicorn 19.3.0 \<pip\>
> h5py 2.7.0 py36he81ebca\_1 defaults
> harfbuzz 1.5.0 h2545bd6\_0 defaults
> hdf5 1.10.1 hb0523eb\_0 defaults
> heapdict 1.0.0 py36h79797d7\_0 defaults
> html5lib 0.999999999 py36h2cfc398\_0 defaults
> icu 58.2 h211956c\_0 defaults
> idna 2.6 py36h82fb2a8\_1 defaults
> imageio 2.2.0 py36he555465\_0 defaults
> imagesize 0.7.1 py36h52d8127\_0 defaults
> importmagic 0.1.7 \<pip\>
> intel-openmp 2018.0.0 h15fc484\_7 defaults
> ipykernel 4.6.1 py36hbf841aa\_0 defaults
> ipython 6.1.0 py36hc72a948\_1 defaults
> ipython\_genutils 0.2.0 py36hb52b0d5\_0 defaults
> ipywidgets 7.0.0 py36h7b55c3a\_0 defaults
> isort 4.2.15 py36had401c0\_0 defaults
> itsdangerous 0.24 py36h93cc618\_1 defaults
> jbig 2.1 hdba287a\_0 defaults
> jdcal 1.3 py36h4c697fb\_0 defaults
> jedi 0.11.1 \<pip\>
> jedi 0.10.2 py36h552def0\_0 defaults
> Jinja2 2.8.1 \<pip\>
> jinja2 2.9.6 py36h489bce4\_1 defaults
> jpeg 9b habf39ab\_1 defaults
> jsonschema 2.6.0 py36h006f8b5\_0 defaults
> jupyter 1.0.0 py36h9896ce5\_0 defaults
> jupyter\_client 5.1.0 py36h614e9ea\_0 defaults
> jupyter\_console 5.2.0 py36he59e554\_1 defaults
> jupyter\_core 4.3.0 py36h357a921\_0 defaults
> jupyterlab 0.27.0 py36h86377d0\_2 defaults
> jupyterlab\_launcher 0.4.0 py36h4d8058d\_0 defaults
> lazy-object-proxy 1.3.1 py36h10fcdad\_0 defaults
> libedit 3.1 heed3624\_0 defaults
> libffi 3.2.1 h4deb6c0\_3 defaults
> libgcc-ng 7.2.0 hcbc56d2\_1 defaults
> libgfortran-ng 7.2.0 h6fcbd8e\_1 defaults
> libpng 1.6.32 hda9c8bc\_2 defaults
> libsodium 1.0.13 h31c71d8\_2 defaults
> libspatialindex 1.8.5 1 conda-forge
> libssh2 1.8.0 h8c220ad\_2 defaults
> libstdcxx-ng 7.2.0 h24385c6\_1 defaults
> libtiff 4.0.8 h90200ff\_9 defaults
> libtool 2.4.6 hd50d1a6\_0 defaults
> libxcb 1.12 he6ee5dd\_2 defaults
> libxml2 2.9.4 h6b072ca\_5 defaults
> libxslt 1.1.29 hcf9102b\_5 defaults
> llvmlite 0.20.0 py36\_0 defaults
> locket 0.2.0 py36h787c0ad\_1 defaults
> lockfile 0.12.2 \<pip\>
> lxml 3.8.0 py36h6c6e760\_0 defaults
> lxml 4.1.1 \<pip\>
> lzo 2.10 hc0eb8fc\_0 defaults
> Mako 1.0.7 \<pip\>
> Markdown 2.6.9 \<pip\>
> markupsafe 1.0 py36hd9260cd\_1 defaults
> matplotlib 2.0.2 py36h2acb4ad\_1 defaults
> mccabe 0.6.1 py36h5ad9710\_1 defaults
> mistune 0.7.4 py36hbab8784\_0 defaults
> mkl 2018.0.0 hb491cac\_4 defaults
> mkl-service 1.1.2 py36h17a0993\_4 defaults
> mpc 1.0.3 hf803216\_4 defaults
> mpfr 3.1.5 h12ff648\_1 defaults
> mpmath 0.19 py36h8cc018b\_2 defaults
> msgpack-python 0.4.8 py36hec4c5d1\_0 defaults
> multipledispatch 0.4.9 py36h41da3fb\_0 defaults
> munch 2.2.0 \<pip\>
> navigator-updater 0.1.0 py36h14770f7\_0 defaults
> nb\_anacondacloud 1.4.0 py36\_0 defaults
> nb\_conda 2.2.1 py36h8118bb2\_0 defaults
> nb\_conda\_kernels 2.1.0 py36\_0 defaults
> nbconvert 5.3.1 py36hb41ffb7\_0 defaults
> nbformat 4.4.0 py36h31c9010\_0 defaults
> nbpresent 3.0.2 py36h5f95a39\_1 defaults
> ncurses 6.0 h06874d7\_1 defaults
> networkx 1.11 py36hfb3574a\_0 defaults
> nltk 3.2.4 py36h1a0979f\_0 defaults
> nose 1.3.7 py36hcdf7029\_2 defaults
> notebook 5.0.0 py36h0b20546\_2 defaults
> numba 0.35.0 np113py36\_10 defaults
> numexpr 2.6.2 py36hdd3393f\_1 defaults
> numpy 1.13.1 py36h5bc529a\_2 defaults
> numpydoc 0.7.0 py36h18f165f\_0 defaults
> odo 0.5.1 py36h90ed295\_0 defaults
> olefile 0.44 py36h79f9f78\_0 defaults
> openpyxl 2.4.8 py36h41dd2a8\_1 defaults
> openssl 1.0.2n hb7f436b\_0 defaults
> ordereddict 1.1 \<pip\>
> packaging 16.8 py36ha668100\_1 defaults
> pandas 0.20.3 py36h842e28d\_2 defaults
> pandoc 1.19.2.1 hea2e7c5\_1 defaults
> pandocfilters 1.4.2 py36ha6701b7\_1 defaults
> pango 1.40.11 hedb6d6b\_0 defaults
> parso 0.1.1 \<pip\>
> partd 0.3.8 py36h36fd896\_0 defaults
> patchelf 0.9 hf79760b\_2 defaults
> path.py 10.3.1 py36he0c6f6d\_0 defaults
> pathlib2 2.3.0 py36h49efa8e\_0 defaults
> patsy 0.4.1 py36ha3be15e\_0 defaults
> pcre 8.41 hc71a17e\_0 defaults
> pep8 1.7.0 py36h26ade29\_0 defaults
> pew 1.1.0 \<pip\>
> pexpect 4.2.1 py36h3b9d41b\_0 defaults
> pickleshare 0.7.4 py36h63277f8\_0 defaults
> pillow 4.2.1 py36h9119f52\_0 defaults
> pip 9.0.1 py36h30f8307\_2 defaults
> pipenv 8.3.1 \<pip\>
> pixman 0.34.0 ha72d70b\_1 defaults
> pkginfo 1.4.1 py36h215d178\_1 defaults
> ply 3.10 py36hed35086\_0 defaults
> prettytable 0.7.2 \<pip\>
> prompt\_toolkit 1.0.15 py36h17d85b1\_0 defaults
> psutil 5.2.2 py36h74c8701\_0 defaults
> psutil 4.4.2 \<pip\>
> ptyprocess 0.5.2 py36h69acd42\_0 defaults
> py 1.4.34 py36h0712aa3\_1 defaults
> pycodestyle 2.3.1 py36hf609f19\_0 defaults
> pycosat 0.6.3 py36h0a5515d\_0 defaults
> pycparser 2.18 py36hf9f622e\_1 defaults
> pycrypto 2.6.1 py36h6998063\_1 defaults
> pycurl 7.43.0 py36h5e72054\_3 defaults
> pyflakes 1.5.0 py36h5510808\_1 defaults
> pygeoif 0.7 \<pip\>
> pygments 2.2.0 py36h0d3125c\_0 defaults
> pylint 1.7.2 py36h484ab97\_0 defaults
> PyMySQL 0.8.0 \<pip\>
> pymysql 0.7.11 py36he04d08f\_0 defaults
> pyodbc 4.0.17 py36h999153c\_0 defaults
> pyopenssl 17.2.0 py36h5cc804b\_0 defaults
> pyparsing 2.2.0 py36hee85983\_1 defaults
> pyproj 1.9.5.1 \<pip\>
> pyqt 5.6.0 py36h0386399\_5 defaults
> pysocks 1.6.7 py36hd97a5b1\_1 defaults
> pytables 3.4.2 py36hdce54c9\_1 defaults
> pytest 3.2.1 py36h11ad3bb\_1 defaults
> python 3.6.2 hdfe5801\_15 defaults
> python-daemon 2.1.2 \<pip\>
> python-dateutil 2.6.1 py36h88d3b88\_1 defaults
> python-editor 1.0.3 \<pip\>
> python-nvd3 0.14.2 \<pip\>
> python-slugify 1.1.4 \<pip\>
> pytz 2017.2 py36hc2ccc2a\_1 defaults
> pywavelets 0.5.2 py36he602eb0\_0 defaults
> pyyaml 3.12 py36hafb9ca4\_1 defaults
> pyzmq 16.0.2 py36h3b0cf96\_2 defaults
> qt 5.6.2 h974d657\_12 defaults
> qtawesome 0.4.4 py36h609ed8c\_0 defaults
> qtconsole 4.3.1 py36h8f73b5b\_0 defaults
> qtpy 1.3.1 py36h3691cc8\_0 defaults
> readline 7.0 hac23ff0\_3 defaults
> requests 2.18.4 py36he2e5f8d\_1 defaults
> rope 0.10.5 py36h1f8c17e\_0 defaults
> rtree 0.8.3 py36\_0 conda-forge
> Rtree 0.8.3 \<pip\>
> ruamel\_yaml 0.11.14 py36ha2fb22d\_2 defaults
> scikit-image 0.13.0 py36had3c07a\_1 defaults
> scikit-learn 0.19.0 py36h97ac459\_2 defaults
> scipy 0.19.1 py36h9976243\_3 defaults
> seaborn 0.8.0 py36h197244f\_0 defaults
> setproctitle 1.1.10 \<pip\>
> setuptools 36.5.0 py36he42e2e1\_0 defaults
> Shapely 1.6.3 \<pip\>
> simplegeneric 0.8.1 py36h2cb9092\_0 defaults
> singledispatch 3.4.0.3 py36h7a266c3\_0 defaults
> sip 4.18.1 py36h51ed4ed\_2 defaults
> six 1.10.0 py36hcac75e4\_1 defaults
> smmap2 2.0.3 \<pip\>
> snowballstemmer 1.2.1 py36h6febd40\_0 defaults
> SoftLayer 5.2.15 \<pip\>
> sortedcollections 0.5.3 py36h3c761f9\_0 defaults
> sortedcontainers 1.5.7 py36hdf89491\_0 defaults
> sphinx 1.6.3 py36he5f0bdb\_0 defaults
> sphinxcontrib 1.0 py36h6d0f590\_1 defaults
> sphinxcontrib-websupport 1.0.1 py36hb5cb234\_1 defaults
> spyder 3.2.3 py36he38cbf7\_1 defaults
> sqlalchemy 1.2.1 py36h14c3975\_0 defaults
> sqlite 3.20.1 h6d8b0f3\_1 defaults
> statsmodels 0.8.0 py36h8533d0b\_0 defaults
> sympy 1.1.1 py36hc6d1c1c\_0 defaults
> tabulate 0.7.7 \<pip\>
> tblib 1.3.2 py36h34cf8b6\_0 defaults
> terminado 0.6 py36ha25a19f\_0 defaults
> testpath 0.3.1 py36h8cadb63\_0 defaults
> thrift 0.9.3 \<pip\>
> tk 8.6.7 h5979e9b\_1 defaults
> toolz 0.8.2 py36h81f2dff\_0 defaults
> tornado 4.5.2 py36h1283b2a\_0 defaults
> traitlets 4.3.2 py36h674d592\_0 defaults
> typing 3.6.2 py36h7da032a\_0 defaults
> unicodecsv 0.14.1 py36ha668878\_0 defaults
> Unidecode 0.04.21 \<pip\>
> unixodbc 2.3.4 hc36303a\_1 defaults
> urllib3 1.22 py36hbe7ace6\_0 defaults
> virtualenv 15.1.0 \<pip\>
> virtualenv-clone 0.2.6 \<pip\>
> wcwidth 0.1.7 py36hdf4376a\_0 defaults
> webencodings 0.5.1 py36h800622e\_1 defaults
> werkzeug 0.12.2 py36hc703753\_0 defaults
> wheel 0.29.0 py36he7f4e38\_1 defaults
> widgetsnbextension 3.0.2 py36hd01bb71\_1 defaults
> wrapt 1.10.11 py36h28b7045\_0 defaults
> WTForms 2.1 \<pip\>
> xlrd 1.1.0 py36h1db9f0c\_1 defaults
> xlsxwriter 0.9.8 py36hf41c223\_0 defaults
> xlwt 1.3.0 py36h7b00a1f\_0 defaults
> xz 5.2.3 h2bcbf08\_1 defaults
> yaml 0.1.7 h96e3832\_1 defaults
> yapf 0.20.0 \<pip\>
> zeromq 4.2.2 hb0b69da\_1 defaults
> zict 0.1.2 py36ha0d441b\_0 defaults
> zlib 1.2.11 hfbfcf68\_1 defaults
> zope.deprecation 4.3.0 \<pip\>
> \`\`\`
> \</p\>\</details\>

I’ve read the suggested reply at

> <https://github.com/conda/conda/issues/6810>
>
> \*\*I'm submitting a...\*\* (I don't know whether it is a bug or feature)
> - \[x\] b…ug report
> - \[x\] feature request
> 
> 
> \## Current Behavior
> 
> 
> 
> \### Steps to Reproduce
> 
> Create an environment, 'test' using Conda 4.4, open a new tab and directly activate that environment. Now try to invoke conda commands using any non shell program (lua/python/java/....) it will error out saying \`conda: command not found\` or \`No such file or directory\` since they can't \`exec()\` that.
> 
> \## Expected Behavior
> 
> The program invoking conda should not error out, or should have a way to figure out where the conda program resides, so that it can exec the full \`/path/to/conda\`. Currently the only thing close to this is \`$\_CONDA\_EXE\`, but it is not documented, and also not exported, so not available to child processes and no guarantee whether it will be available in future releases.
> 
> The current work around is to first activate the base environment and then activate the non-base environment in the same shell session, which for whatever reason, retains the root environment's bin directory in the PATH.

but can’t make sense of it.

I understand that we prefer to containerise conda installs these days, from [Conda hh5 environment setup — CLEX CMS Wiki](https://coecms.github.io/cms-wiki/resources/resources-conda-setup.html) (and Scott Wales’ template) but that’s isn’t going to solve our immediate problem.

The only activate script I can find in this new environment is  
`/scratch/nf33/public/miniconda/envs/digital_earths_env/lib/python3.12/venv/scripts/common/activate`

Now - before I create a symlink to `/bin/activate` to that file (and I’m afraid of unintended consequences), does anyone have a work-around?

Or is that the solution? I’ve noted the `hh5 bin/activate` file is very different to `envs/digital_earths_env/lib/python3.12/venv/scripts/common/activate`.

Currently- if I specify this to ARE

 ![Screenshot 2025-05-12 at 4.41.56 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/6/6cf7cd4d4687a2e327eb27c7149bba755ee9cafb.png)

ARE can find the `bin/jupyter` directory

 ![Screenshot 2025-05-12 at 5.28.54 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/c/c55f43af89c279ddedda881b7578a42942f4c060.png)

But no kernels are available.

EDIT : A temporary work-around was to build a python virtual environment on top of the conda environment.

```auto
python -m venv digital_earths_venv 
source /scratch/nf33/public/digital_earths_venv/bin/activate
python -m ipykernel install --prefix /scratch/nf33/public/digital_earths_venv --name digital_earths_venv --display-name "digital_earths_kernel"
cd ~/.local/share/jupyter/kernels/
ln -s /scratch/nf33/public/digital_earths_venv/share/jupyter/kernels/digital_earths_venv

```

This allows the digital earth conda environment to be loaded into ARE.

But surely there must be an easier way?

Mods - this topic is smilier to [How to create a personal Conda environment on Gadi when you really need one?](https://forum.access-hive.org.au/t/how-to-create-a-personal-conda-environment-on-gadi-when-you-really-need-one/1727) so feel free to merge if required.

---

<div class="post-metadata">

**Author:** ![Scott](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/scott/32/37_2.png) [@Scott](https://forum.access-hive.org.au/u/Scott)\
**Post date:** [12 May 2025 23:43 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/2 "2025-05-12T23:43:10Z")

</div>

Environment activation can be manually done with

```bash
eval $($CONDA_PREFIX/bin/conda shell.bash activate ENV)

```

(this is what `conda activate` runs), you could put that in a new script file `$CONDA_PREFIX/bin/activate` and point the virtual environment base to `$CONDA_PREFIX`.

The `activate` script you found is part of the `venv` package, it would be for activating virtual environments rather than conda environments.

---

<div class="post-metadata">

**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\
**Post date:** [13 May 2025 03:41 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/3 "2025-05-13T03:41:41Z")

</div>

Thanks a lot Scott for that explanation.

We are running with the extra virtual environment at the moment, I will test your solution when I can.

---

<div class="post-metadata">

**Author:** ![jemmajeffree](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/jemmajeffree/32/228_2.png) [@jemmajeffree](https://forum.access-hive.org.au/u/jemmajeffree)\
**Post date:** [13 May 2025 04:45 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/4 "2025-05-13T04:45:14Z")

</div>

Hi Paul,  
Based on my interactions on my local machine, and what I can see of your conda, it looks like the “Python or Conda virtual environment base” should be `/scratch/nf33/public/miniconda/` (looking for `/scratch/nf33/public/miniconda/bin/activate`) and even though it doesn’t specify the environment I think this would give you options for a kernel of digital\_earths\_env, assuming that either ipykernel or jupyterlab is installed.  
I can’t test this at the moment (I’m not part of nf33) but I will once I can.

---

<div class="post-metadata">

**Author:** ![jemmajeffree](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/jemmajeffree/32/228_2.png) [@jemmajeffree](https://forum.access-hive.org.au/u/jemmajeffree)\
**Post date:** [13 May 2025 05:20 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/5 "2025-05-13T05:20:37Z")

</div>

I think I have a conda working with your environment.  
Python or Conda virtual environment base: `/scratch/nf33/public/miniconda`  
Conda environment: `digital_earths_env`

 ![Screenshot 2025-05-13 at 3.16.15 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/c/c975043aada18425ded7378622209cbc6c2ab50b.png)  
 ![Screenshot 2025-05-13 at 3.16.24 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/2/2510a2b39793e5c8b22b31e584a06abd10c13810.png)  
 ![Screenshot 2025-05-13 at 3.19.57 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/optimized/2X/2/20bd2d04c3cfb20d48a2e8f4d73a27c131139c4d_2_690x49.png)  
 ![Screenshot 2025-05-13 at 3.20.23 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/d/d28bfc1827e77faf3f350f858de673bdc7c6bc14.png)

---

<div class="post-metadata">

**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\
**Post date:** [13 May 2025 05:40 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/6 "2025-05-13T05:40:41Z")

</div>

Hi @jemmajeffree

Which kernel have you selected? What other kernels can you select?

---

<div class="post-metadata">

**Author:** ![jemmajeffree](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/jemmajeffree/32/228_2.png) [@jemmajeffree](https://forum.access-hive.org.au/u/jemmajeffree)\
**Post date:** [13 May 2025 05:42 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/7 "2025-05-13T05:42:08Z")

</div>

I selected something with a bunch of random numbers and letters (bdccf2dc), and I only had the one option, which surprised me

---

<div class="post-metadata">

**Author:** ![Paul.Gregory](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paul.gregory/32/2566_2.png) [@Paul.Gregory](https://forum.access-hive.org.au/u/Paul.Gregory)\
**Post date:** [13 May 2025 06:02 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/8 "2025-05-13T06:02:20Z")

</div>

Ah. I have learnt something.

I have six kernels available. Five of them are in my `~/.local/share/jupyter/kernels/` directory. The sixth is the ‘Python 3 (ipkernel)’.

 ![Screenshot 2025-05-13 at 3.42.52 pm](https://us1.discourse-cdn.com/flex020/uploads/access1/original/2X/7/7decdb77d07c48e3f1b615d1a0b290b1841b6939.png)

When I used previous ARE environments, the default kernel was usually linked to a standard python installation which didn’t have any of the required modules.

However, I now realise the ‘Python 3 (ipkernel)’ is actually located in  
`/scratch/nf33/public/miniconda/envs/digital_earths_env/share/jupyter/kernels/python3/kernel.json`

```auto
more /scratch/nf33/public/miniconda/envs/digital_earths_env/share/jupyter/kernels/python3/kernel.json

{
 "argv": [
  "/scratch/nf33/public/miniconda/envs/digital_earths_env/bin/python",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "Python 3 (ipykernel)",
 "language": "python",
 "metadata": {
  "debugger": true
 }
}

```

So in this case, the default Python3 kernel works fine. So I didn’t need to build another virtual environment on top of it.

Thanks for the investigation.

---

<div class="post-metadata">

**Author:** ![Scott](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/scott/32/37_2.png) [@Scott](https://forum.access-hive.org.au/u/Scott)\
**Post date:** [13 May 2025 06:04 UTC](https://forum.access-hive.org.au/t/getting-custom-conda-environment-loaded-into-are-environment/4499/9 "2025-05-13T06:04:05Z")

</div>

You can install the conda pacakge `nb_conda_kernels` in the same environment as jupyterlab if you want to be able to select kernels from other environments (you probably don’t need to enable this for your hackathon)