Current environments
====================

.. tip::

   **Contact** `Secretariat System Administrators`_ **with HPC Questions!**

   +------------------+----------------+--------------------+
   | `Vijay Shankar`_ | `John Poole`_  | `Maria E. Adonay`_ |
   +------------------+----------------+--------------------+

   .. code-block:: text

      vshanka@clemson.edu,jopoole@clemson.edu,madonay@clemson.edu

   .. raw:: html

      <hr>

   **Contact** `IHG Research Cores`_ **with Research Questions!**

   .. code-block:: text

      ihgcores@clemson.edu

----

This is a table of cluster-wide environments on Secretariat.

.. attention::

   This list is updated only periodically. For a full, current list, log in to Secretariat and run the following commands:

   .. code-block:: bash

      source /opt/ohpc/pub/Software/mamba-rocky/etc/profile.d/conda.sh
      source /opt/ohpc/pub/Software/mamba-rocky/etc/profile.d/mamba.sh
      mamba env list

----

+-------------------------+
| Environment             |
+=========================+
| Admixfrog               |
+-------------------------+
| CADD_test               |
+-------------------------+
| IQ-Tree                 |
+-------------------------+
| JO                      |
+-------------------------+
| LDBlockShow             |
+-------------------------+
| RNAvigate               |
+-------------------------+
| alpha_diversity         |
+-------------------------+
| argweaver_d             |
+-------------------------+
| bic_flows               |
+-------------------------+
| conda_pack              |
+-------------------------+
| eigensoft               |
+-------------------------+
| exon_skipping           |
+-------------------------+
| fastqwiper              |
+-------------------------+
| flask                   |
+-------------------------+
| gcc9_libstdc6           |
+-------------------------+
| humann_3.9_pip          |
+-------------------------+
| iJulia                  |
+-------------------------+
| justortho               |
+-------------------------+
| manta                   |
+-------------------------+
| masurca                 |
+-------------------------+
| mirdeep2                |
+-------------------------+
| msprime                 |
+-------------------------+
| multiqc                 |
+-------------------------+
| nextflow                |
+-------------------------+
| nextflow_23.04.1        |
+-------------------------+
| notebook_env            |
+-------------------------+
| notebook_env_backup     |
+-------------------------+
| ood_env                 |
+-------------------------+
| pandas                  |
+-------------------------+
| pcangsd                 |
+-------------------------+
| pggb                    |
+-------------------------+
| picrust2                |
+-------------------------+
| plotly                  |
+-------------------------+
| pod5                    |
+-------------------------+
| pyFasta                 |
+-------------------------+
| pysam                   |
+-------------------------+
| pytorch_idebnat         |
+-------------------------+
| pytorch_test            |
+-------------------------+
| pyvcf                   |
+-------------------------+
| qualimap_angsd          |
+-------------------------+
| r-reticulate            |
+-------------------------+
| r_asc_seurat            |
+-------------------------+
| rapids-23.04            |
+-------------------------+
| rfmix2                  |
+-------------------------+
| ribotaper               |
+-------------------------+
| rmats                   |
+-------------------------+
| rustenv                 |
+-------------------------+
| s3-tree                 |
+-------------------------+
| sailfish                |
+-------------------------+
| samtools                |
+-------------------------+
| seqkit                  |
+-------------------------+
| seqtk                   |
+-------------------------+
| shapeit4                |
+-------------------------+
| snakemake               |
+-------------------------+
| sniffles2               |
+-------------------------+
| spipe                   |
+-------------------------+
| spyder-env              |
+-------------------------+
| survivor                |
+-------------------------+
| trimgalore              |
+-------------------------+
| vep                     |
+-------------------------+
| vs_emacs                |
+-------------------------+

List last updated: 11 November 2025.

.. _Vijay Shankar: https://scienceweb.clemson.edu/chg/dr-vijay-shankar-2/
.. _John Poole: https://scienceweb.clemson.edu/chg/dr-john-poole/
.. _Maria E. Adonay: https://scienceweb.clemson.edu/chg/maria-adonay/
.. _Secretariat System Administrators: https://scienceweb.clemson.edu/ihg/research-cores/bsc-core/
.. _IHG Research Cores: https://scienceweb.clemson.edu/ihg/research-cores/