Current software
================

.. 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 the modularized software on Secretariat.

.. attention::
   
   This list is updated only periodically. For a full, current list, log in to Secretariat and run the command ``module avail``. For more information on software modularization, see the `Software modularization`_ page.

----

+-----------------------+--------------------------------------------------+
| Software              | Version                                          |
+=======================+==================================================+
| abblast               | 3.0                                              |
+-----------------------+--------------------------------------------------+
| afterqc               | 0.9.7                                            |
+-----------------------+--------------------------------------------------+
| adios                 | 1.13.1                                           |
+-----------------------+--------------------------------------------------+
| argweaver             | 50bbd3c                                          |
+-----------------------+--------------------------------------------------+
| augustus              | 3.3.3                                            |
+-----------------------+--------------------------------------------------+
| autotools             |                                                  |
+-----------------------+--------------------------------------------------+
| bamtools              | 1.0                                              |
+-----------------------+--------------------------------------------------+
| bbmap                 | 38.73                                            |
+-----------------------+--------------------------------------------------+
| bedops                | 2.4.40                                           |
+-----------------------+--------------------------------------------------+
| bedtools2             | 2.29.2                                           |
+-----------------------+--------------------------------------------------+
| blast                 | 2.9.0                                            |
+-----------------------+--------------------------------------------------+
| bowtie1               | 1.2.0-py27_0                                     |
+-----------------------+--------------------------------------------------+
| bowtie2               | 2.2.5                                            |
+-----------------------+--------------------------------------------------+
| busco                 | 2.0.1                                            |
+-----------------------+--------------------------------------------------+
| bwa                   | 0.7.17                                           |
+-----------------------+--------------------------------------------------+
| cd-hit                | 4.8.1                                            |
+-----------------------+--------------------------------------------------+
| cellranger            | 3.1.0, 7.0.1                                     |
+-----------------------+--------------------------------------------------+
| cellranger-arc        | 2.0.2                                            |
+-----------------------+--------------------------------------------------+
| centos_compat         | 1.0.0                                            |
+-----------------------+--------------------------------------------------+
| charliecloud          | 0.9.2, 0.15                                      |
+-----------------------+--------------------------------------------------+
| cmake                 | 3.12.2, 3.21.3                                   |
+-----------------------+--------------------------------------------------+
| conda                 | 2.0.1                                            |
+-----------------------+--------------------------------------------------+
| cufflinks             | 2.2.1                                            |
+-----------------------+--------------------------------------------------+
| cutadapt              | 1.18                                             |
+-----------------------+--------------------------------------------------+
| delly                 | 0.8.3                                            |
+-----------------------+--------------------------------------------------+
| dorado                | 0.9.1                                            |
+-----------------------+--------------------------------------------------+
| easybuild             | 3.7.1                                            |
+-----------------------+--------------------------------------------------+
| EasyBuild             | 4.5.0                                            |
+-----------------------+--------------------------------------------------+
| exonerate             | 2.4.0                                            |
+-----------------------+--------------------------------------------------+
| fastp                 | 0.21.0                                           |
+-----------------------+--------------------------------------------------+
| fastqc                | 0.11.9                                           |
+-----------------------+--------------------------------------------------+
| fastqvalidator        | 0.1.1                                            |
+-----------------------+--------------------------------------------------+
| ffmpeg                | N-99555-g00772ef                                 |
+-----------------------+--------------------------------------------------+
| fftw                  | 3.3.8                                            |
+-----------------------+--------------------------------------------------+
| flash                 | 1.2.11                                           |
+-----------------------+--------------------------------------------------+
| gatk                  | 4.1.4.1                                          |
+-----------------------+--------------------------------------------------+
| gcc                   | 10.1.0, 12.2.0                                   |
+-----------------------+--------------------------------------------------+
| gcta                  | 1.93.2, 1.94.1                                   |
+-----------------------+--------------------------------------------------+
| gdc-client            | 1.6.1                                            |
+-----------------------+--------------------------------------------------+
| gemma                 | 0.98.5                                           |
+-----------------------+--------------------------------------------------+
| genometools           | 1.5.9                                            |
+-----------------------+--------------------------------------------------+
| gffcompare            | 0.11.2                                           |
+-----------------------+--------------------------------------------------+
| gffread               | 0.11.6, 0.12.7                                   |
+-----------------------+--------------------------------------------------+
| gmap_gsnap            | 2019.09.12                                       |
+-----------------------+--------------------------------------------------+
| gsl                   | 2.5, 2.7                                         |
+-----------------------+--------------------------------------------------+
| gsutil                | 4.47                                             |
+-----------------------+--------------------------------------------------+
| hdf5                  | 1.10.3, 1.10.8                                   |
+-----------------------+--------------------------------------------------+
| hisat2                | 2.1.0                                            |
+-----------------------+--------------------------------------------------+
| hmmer                 | 3.1b2                                            |
+-----------------------+--------------------------------------------------+
| htop                  | 3.0.5                                            |
+-----------------------+--------------------------------------------------+
| htseq                 | 0.11.2                                           |
+-----------------------+--------------------------------------------------+
| hwloc                 | 1.11.10, 2.5.0                                   |
+-----------------------+--------------------------------------------------+
| iribo                 | carvunislab                                      |
+-----------------------+--------------------------------------------------+
| java_jdk              | 1.8.231, 11.0.2                                  |
+-----------------------+--------------------------------------------------+
| lemma                 | 1.0.0                                            |
+-----------------------+--------------------------------------------------+
| libStatGen            | 1.0.5                                            |
+-----------------------+--------------------------------------------------+
| libboost              | 1.72.0                                           |
+-----------------------+--------------------------------------------------+
| libfabric             | 1.13.0                                           |
+-----------------------+--------------------------------------------------+
| libiconv              | 1.17                                             |
+-----------------------+--------------------------------------------------+
| likwid                | 4.3.2, 5.0.1                                     |
+-----------------------+--------------------------------------------------+
| linearpartition       | 1.0                                              |
+-----------------------+--------------------------------------------------+
| ltr_retriever         | 2.6                                              |
+-----------------------+--------------------------------------------------+
| mafft                 | 7.453                                            |
+-----------------------+--------------------------------------------------+
| maker                 | 2.31.9, 2.31.10                                  |
+-----------------------+--------------------------------------------------+
| mauve                 | 2.4.0                                            |
+-----------------------+--------------------------------------------------+
| mauvealigner          | 1.2.0                                            |
+-----------------------+--------------------------------------------------+
| mfem                  | 3.4, 4.3                                         |
+-----------------------+--------------------------------------------------+
| metis                 | 5.1.0                                            |
+-----------------------+--------------------------------------------------+
| mpiP                  | 3.4.1                                            |
+-----------------------+--------------------------------------------------+
| mpich                 | 3.2.1, 3.4.2-ofi                                 |
+-----------------------+--------------------------------------------------+
| mvapich2              | 2.3, 2.3.6                                       |
+-----------------------+--------------------------------------------------+
| multiqc               | 1.7                                              |
+-----------------------+--------------------------------------------------+
| netcdf                | 4.6.1, 4.7.4                                     |
+-----------------------+--------------------------------------------------+
| netcdf-cxx            | 4.3.0, 4.3.1                                     |
+-----------------------+--------------------------------------------------+
| netcdf-fortran        | 4.4.4, 4.5.3                                     |
+-----------------------+--------------------------------------------------+
| ninja                 | 0.95_co                                          |
+-----------------------+--------------------------------------------------+
| nvidia/cuda           | 12.5.0                                           |
+-----------------------+--------------------------------------------------+
| ohpc                  |                                                  |
+-----------------------+--------------------------------------------------+
| openblas              | 0.3.0, 0.3.7, 0.3.10                             |
+-----------------------+--------------------------------------------------+
| opencoarrays          | 2.2.0, 2.9.2                                     |
+-----------------------+--------------------------------------------------+
| openmpi3              | 3.1.2                                            |
+-----------------------+--------------------------------------------------+
| openmpi4              | 4.1.1                                            |
+-----------------------+--------------------------------------------------+
| pdtoolkit             | 3.25, 3.25.1                                     |
+-----------------------+--------------------------------------------------+
| papi                  | 5.6.0, 5.7.0                                     |
+-----------------------+--------------------------------------------------+
| pbmm2                 | 1.2.1                                            |
+-----------------------+--------------------------------------------------+
| pbsv                  | 2.3.0                                            |
+-----------------------+--------------------------------------------------+
| picard                | 2.21.7                                           |
+-----------------------+--------------------------------------------------+
| plink                 | 1.90b6.20                                        |
+-----------------------+--------------------------------------------------+
| plasma                | 2.8.0                                            |
+-----------------------+--------------------------------------------------+
| pmix                  | 2.1.4                                            |
+-----------------------+--------------------------------------------------+
| prun                  | 1.2, 2.2                                         |
+-----------------------+--------------------------------------------------+
| python2.7-fm          | 2.7.18                                           |
+-----------------------+--------------------------------------------------+
| python3.8             | 3.8.4                                            |
+-----------------------+--------------------------------------------------+
| py2-numpy             | 1.15.1                                           |
+-----------------------+--------------------------------------------------+
| py2-mpi4py            | 3.0.0                                            |
+-----------------------+--------------------------------------------------+
| py2-scipy             | 1.1.0                                            |
+-----------------------+--------------------------------------------------+
| py3-mpi4py            | 3.0.0, 3.0.3                                     |
+-----------------------+--------------------------------------------------+
| py3-numpy             | 1.15.1, 1.19.5                                   |
+-----------------------+--------------------------------------------------+
| py3-scipy             | 1.1.0, 1.5.1                                     |
+-----------------------+--------------------------------------------------+
| readline              | 8.0                                              |
+-----------------------+--------------------------------------------------+
| recon                 | 1.08                                             |
+-----------------------+--------------------------------------------------+
| regtools              | 0.5.0                                            |
+-----------------------+--------------------------------------------------+
| repeatmasker          | 4.1.0                                            |
+-----------------------+--------------------------------------------------+
| repeatscout           | 1.0.6                                            |
+-----------------------+--------------------------------------------------+
| rmblast               | 2.9.0-p2                                         |
+-----------------------+--------------------------------------------------+
| rmtgenenet            | 1.0                                              |
+-----------------------+--------------------------------------------------+
| R                     | 3.5.0, 3.6.1, 4.0.3, 4.1.2, 4.2.1, 4.2.3, 4.3.0  |
+-----------------------+--------------------------------------------------+
| rnastructure          | 6.2, 6.5                                         |
+-----------------------+--------------------------------------------------+
| rsem                  | 1.3.2                                            |
+-----------------------+--------------------------------------------------+
| samtools              | 1.9, 1.10                                        |
+-----------------------+--------------------------------------------------+
| scalapack             | 2.0.2, 2.1.0                                     |
+-----------------------+--------------------------------------------------+
| scalasca              | 2.4, 2.5                                         |
+-----------------------+--------------------------------------------------+
| shapeit2              | 2.0.0                                            |
+-----------------------+--------------------------------------------------+
| shapemapper           | 2.1.5, 2.2.0                                     |
+-----------------------+--------------------------------------------------+
| shapewarp             | 1.0                                              |
+-----------------------+--------------------------------------------------+
| sionlib               | 1.7.2, 1.7.4                                     |
+-----------------------+--------------------------------------------------+
| singularity           | 2.6.0, 3.7.1                                     |
+-----------------------+--------------------------------------------------+
| snap                  | 11.29.2013                                       |
+-----------------------+--------------------------------------------------+
| sra                   | 2.11.0                                           |
+-----------------------+--------------------------------------------------+
| stack                 | 2.3.3                                            |
+-----------------------+--------------------------------------------------+
| star                  | 2.7.3a-0, 2.7.10a                                |
+-----------------------+--------------------------------------------------+
| stringtie             | 2.0                                              |
+-----------------------+--------------------------------------------------+
| subread               | 1.6.4                                            |
+-----------------------+--------------------------------------------------+
| superfold             | 1.0                                              |
+-----------------------+--------------------------------------------------+
| superlu               | 5.2.1                                            |
+-----------------------+--------------------------------------------------+
| superlu_dist          | 5.4.0, 6.4.0                                     |
+-----------------------+--------------------------------------------------+
| texlive               | 53254-2019.12.29                                 |
+-----------------------+--------------------------------------------------+
| tophat                | 2.1.1                                            |
+-----------------------+--------------------------------------------------+
| trf                   | 4.0.9                                            |
+-----------------------+--------------------------------------------------+
| trimmomatic           | 0.39-1                                           |
+-----------------------+--------------------------------------------------+
| trilinos              | 12.12.1, 13.2.0                                  |
+-----------------------+--------------------------------------------------+
| trinity               | 2.1.1-6                                          |
+-----------------------+--------------------------------------------------+
| trinotate             | 3.2.0                                            |
+-----------------------+--------------------------------------------------+
| tau                   | 2.27.1, 2.29                                     |
+-----------------------+--------------------------------------------------+
| ucx                   | 1.11.2                                           |
+-----------------------+--------------------------------------------------+
| valgrind              | 3.13.0, 3.18.1                                   |
+-----------------------+--------------------------------------------------+
| vbt                   | 1.1                                              |
+-----------------------+--------------------------------------------------+
| vcftools              | 0.1.16                                           |
+-----------------------+--------------------------------------------------+
| viennarna             | 2.4.18                                           |
+-----------------------+--------------------------------------------------+
| xclip                 | 0.13                                             |
+-----------------------+--------------------------------------------------+
| yasm                  | 1.2.0                                            |
+-----------------------+--------------------------------------------------+


List last updated: 11 November 2025.

.. _Software modularization: https://secretariat.readthedocs.io/en/latest/compute/modules.html#software-modularization
.. _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/