.. include:: uantwerp_links.rst

.. _Antwerp software 2020a:

UAntwerp 2020a toolchains
=========================

Most software packages in use on leibniz were reinstalled in the 2020a toolchains,
which are the initial toolchains for the Vaughan cluster. Many packages were updated
to their most recent versions.

Searching for installed software
--------------------------------

At UAntwerp, Lmod is the environment module system to manage the software available to
the users since 2017.

One advantage of Lmod over the software we used before, is much more powerful search for
installed software. Search is also case-insensitive, so you do not need to know if capitals
are used in the module name or not to find the correct name and version of a module.

There are three commands to search for a module:

#. Search in the list of activated modules (those modules that can be loaded without first
   loading another `calcua`` module)::

       $ module av Python

   will search for an activated module whose name or version string contains ``Python``.

#. Search in the list of all available modules, including those that require loading other
   modules first::

      $ module spider Python

   If you need more information about the module, including which modules you might need to load,
   you can use::

      $ module spider Python/3.8.3-intel-2020a

   The explanation in the output about the module(s) that need to be loaded to actually use
   that Python module, can be a bit confusing. You have to take one line from the output and load
   all modules on that line (and in most cases one module will be sufficient).

#. Each module also contains a limited amount of additional information that can be shown with
   the ``module whatis`` command, e.g.::

      $ module whatis Python/3.8.3-intel-2020a

   It is possible to search through all the 'whatis'-information of installed modules using ``module keyword``::

      $ module keyword CMake

   This is a pretty powerful way to search for installed software. Whenever we put several related
   software packages together in a single module, we try to make sure that that software can be found
   through ``module keyword``. Unfortunately, though the software that we use to install packages and to
   generate the modules in a consistent way, does not yet allow us to easily generate a list of the extensions
   included in modules such as ``Python``, ``Perl`` or ``R``. The output of ``module spider`` for s specific
   version number will usually show the included packages (with very few exceptions where we needed to use
   special tricks to install the packages).



Overview of modules
-------------------

The first column is the name of the module. The second column contains the most recent version
of the module installed in the pre-2020a toolchains. The third column then shows the version(s) offered
in the 2020a toolchains or refers to an alternative.

+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Package                  | Last version                                 | 2020a version                                         |
+==========================+==============================================+=======================================================+
| `ABINIT`_                | 8.10.2-intel-2016b-hybrid-mkl                | - 8.10.3-intel-2020a-hybrid-mkl                       |
|                          |                                              | - 9.0.4-intel-2020a-hybrid-mkl                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ACTC`_                  | 1.1-GCCcore-8.3.0                            | 1.1-GCCcore-9.3.0                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Amber`_                 | 18-intel-2019b-AmberTools-19-patchlevel-17-9 | - 18-intel-2019b-AmberTools-19-patchlevel-17-12       |
|                          |                                              | - 20-intel-2020a-AmberTools-20-patchlevel-6-10        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ANSYS`_                 | 17.2                                         | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ant`_                   | 1.10.1-Java-8                                | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ANTs`_                  | 2.3.2-intel-2019b                            | 2.3.3-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `arpack-ng`_             | 3.6.3-intel-2019b                            | 3.6.3-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ASE`_                   | 3.18.1-intel-2019b-Python-3.7.4              | 3.19.1-intel-2020a-\*                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `atools`_                | 1.4.7                                        | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Autoconf                 | 2.69                                         | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| AutoDock_Vina            | 1.1.2                                        | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Automake                 | 1.15                                         | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Autotools                | 20161231                                     | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| BALi-Phy                 | 3.0-beta4-intel-2017a-sequential             | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| baselibs                 | 2019b-GCCcore-8.3.0                          | 2020a-GCCcore-9.3.0                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Bazel                    | 0.5.3                                        | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| BCFtools                 | 1.10.2-intel-2019b                           | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| bcl2fastq2               | 2.20.0-intel-2018b                           | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `beagle-lib`_            | 3.1.2-intel-2019b(-OpenMP)                   | 3.1.2-intel-202020a(-OpenMP)                          |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Beast`_                 | 2.6.0-intel-2019b                            | 2.6.2-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| BEDtools                 | 2.27.1-intel-2018b                           | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| behave                   | 1.2.5-intel-2017a-Python-2.7.13              | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `BerkeleyGW`_            | 2.1-intel-2019b-hybrid                       | 2.1-intel-2020a-hybrid                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| binutils                 | 2.32-GCCcore-8.3.0                           | 2.34-GCCcore-9.3.0                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `BioPerl`_               | 1.7.2-intel-2018b-Perl-5.26.1                | 1.7.7-intel-2020a-Perl-5.30.2                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Biopython                | 1.74-intel-2019b-Python-3.7.4                | Moved into BioTools-Python/2020a.00-intel-2020a-\*    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Bismark`_               | 0.22.1-intel-2019b                           | 0.22.3-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Bison                    | 3.0.5                                        | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `BLAST+`_                | 2.9.0-intel-2018b-Python-3.7.1               | 2.10.0-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| BoltzTraP                | 1.2.5-intel-2018a                            | Installed on demand (suggestion: BoltzTraP2)          |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Boost`_                 | 1.70.0-intel-2019b                           | 1.73.0-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Bowtie2`_               | 2.3.5.1-intel-2019b                          | 2.4.1-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| buildtools               | 2019b                                        | 2020a                                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `BWA`_                   | 0.7.17-intel-2019b                           | 0.7.17-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| byacc                    | 20170201                                     | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| bzip2                    | 1.0.6-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `cairo`_                 | 1.17.2-GCCcore-8.3.0                         | 1.17.2-GCCcore-9.3.0                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `canu`_                  | 1.9-intel-2019b                              | 2.0-intel-2020a                                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| CD-HIT                   | 4.6.8-intel-2018b                            | 4.8.1, moved into BioTools                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| CellRanger               | 2.2.0-intel-2018b                            | Move to system toolchain, need update from the user   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| CellRanger-DNA           | 1.1.0                                        | SYSTEM toolchain, files and license needed            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `CGAL`_                  | 4.10.2-intel-2019b-forOpenFOAM6              | 4.10.2-intel-2020a-forOpenFOAM6                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| ClonalFrameML            | 1.11-intel-2018b                             | 1.12, moved into BioTools                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| CMake                    | 3.9.1                                        | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| COMSOL                   | 5.3                                          | 5.5.0.359                                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| core-counter             | 1.1                                          | 1.1.1 (SYSTEM toolchain)                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `CP2K`_                  | 7.1 in various variants                      | 7.1 in various variants                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `CPMD`_                  | 4.3-intel-2019b                              | 4.3-intel-2020a-pl4624                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| cppcheck                 | 1.83-intel-2018a                             | Installed on demand (and needs Qt5)                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Cube`_                  | 4.3.5-intel-2018a                            | TODO - Awaiting Qt5 which does not compile            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `CUDA`_                  | 10.2.89                                      | 11.1.0                                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `cuDNN`_                 | 7.6.5.32-CUDA-10.1.243                       | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| cURL                     | 7.61.0-intel-2018b                           | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Dacapo                   | 476-intel-2018b                              | Installed on demand, web site outdated                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Dalton                   | 2018.2-intel-2018b-i8                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Darknet                  | 20180326-intel-2018a-*                       | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| darshan-runtime          | 3.1.7-intel-2018b                            | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| darshan-util             | 3.1.7-intel-2018b                            | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| DDSCAT                   | 7.3.2_170125-intel-2018a                     | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Delft3D                  | 7565-intel-2018b                             | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `DFTB+`_                 | 19.1-intel-2019b-Python-2.7.16(-MPI)         | 19.1-intel-2020a-Python-3.8.2(-MPI)                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| DIAMOND                  | 0.9.22-intel-2018a                           | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| DLCpar                   | 1.0-intel-2019b-Python-3.7.4                 | Moved into BioTools-Python/2020a.00-intel-2020a-\*    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| DMTCP                    | 2.6.0                                        | Toolchain-independent?                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Doxygen                  | 1.8.13                                       | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `DSSP`_                  | 2.2.1-intel-2017a                            | 2.3.0-intel-2020a, 3.1.4-intel-2020a                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `EasyBuild`_             | 4.2.0                                        | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `eclipse`_               | parallel-2018-12                             | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Eigen`_                 | 3.3.7-intel-2019b                            | 3.3.7                                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Elk`_                   | 5.2.14-intel-2019b                           | 6.3.2-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ELPA`_                  | 2019.11.001-intel-2019b                      | 2019.11.001-intel-2020a                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ELSI`_                  | 2.5.0-intel-2019b                            | 2.5.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Exonerate                | 2.4.0-intel-2017a                            | Installed on demand (unmaintained)                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| expat                    | 2.2.5-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Faiss                    | 1.5.0-intel-2018b-Python-3.7.1-CPU           | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| FastME                   | 2.1.6.1-intel-2018a                          | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| fastp                    | 0.20.0-intel-2019b                           | Moved to BioTools/2020a.00-intel-2020a                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| FastTree                 | 2.1.10-intel-2018b                           | Moved to BioTools/2020a.00-intel-2020a                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `FFmpeg`_                | 4.1.4 (Intel and GCCcore)                    | 4.2.2 (Intel and GCCcore)                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `FFTW`_                  | 3.3.8-intel-2019b                            | 3.3.38 (Intel 2 versions)                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| file                     | 5.30-intel-2017a                             | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| FINE-Marine              | 5.2                                          | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| flex                     | 2.6.4                                        | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `FLTK`_                  | 1.3.5-GCCcore-8.3.0-viz                      | 1.3.5-GCCcore-9.3.0-viz                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Flye                     | 2.7-intel-2019b-Python-3.7.4                 | Moved into BioTools-Python/2020a.00-intel-2020a-\*    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| fontconfig               | 2.12.6-intel-2018b                           | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| foss                     | 2018b                                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| freetype                 | 2.9-intel-2018a                              | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| FriBidi                  | 1.0.5-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GATK`_                  | 4.1.4.1-Java-8-minimal                       | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Gaussian`_              | Gaussian16/g16_A3-AVX2                       | - g16_a03-avx2                                        |
|                          |                                              | - g16_c01-avx2                                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GaussView`_             | /                                            | 6.1.1                                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| gc                       | 7.6.4-intel-2018a                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GCC`_                   | 8.3.0-2.32                                   | 9.3.0-2.34                                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| GCCcore                  | 8.3.0                                        | 9.3.0                                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GDAL`_                  | 3.0.1-intel-2019b                            | 3.1.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GEOS`_                  | 3.7.2-intel-2019b                            | 3.8.1-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| gettext                  | 0.19.8.1-intel-2018b                         | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Ghostscript`_           | 9.27-GCCcore-8.3.0                           | 9.52-GCCcore-9.3.0                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| git                      | 2.13.3                                       | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GLib`_                  | 2.61.2-GCCcore-8.3.0                         | 2.64.1-GCCcore-9.3.0                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GlobalArrays`_          | /                                            | 5.7.2-intel-2020a-peigs                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GMAP-GSNAP`_            | 2019-06-10-intel-2019b                       | 2020-03-12-intel-2020a                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `g_mmpbsa`_              | 1.6                                          | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `gnuplot`_               | 5.2.7-intel-2019b                            | 5.4.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Go                       | 1.10.1                                       | Updated on demand                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GObject-Introspection`_ | 1.61.1-GCCcore-8.3.0                         | 1.64.1-GCCcore-9.3.0                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| gompi                    | 2018b                                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GPAW`_                  | 19.8.1 (multiple configurations)             | 20.1.0 (multiple configurations)                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `GROMACS`_               | 2019.4-intel-2019b                           | * 2019.4 with PLUMED                                  |
|                          |                                              | * 2020.2-intel-2020a with and without CUDA            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| GSL                      | 2.5-intel-2018b                              | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| gtest                    | 1.8.1 (Intel, GCCcore)                       | 1.10.0-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Guile                    | 2.2.3-intel-2018a-ncurses                    | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Gurobi                   | 9.0.0                                        | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| hanythingondemand        | 3.2.0-intel-2017a-Python-2.7.13              | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `HarfBuzz`_              | 2.5.3-GCCcore-8.3.0                          | 2.6.4-GCCcore-9.3.0                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `HDF5`_                  | 1.10.5-intel-2019b-MPI (and 1.8.21)          | 1.12.0-intel-2020a-MPI (and 1.10.6)                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| HEEDS                    | 2018.10                                      | Installed on demand (SimCenter option).               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| help2man                 | 1.47.5                                       | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| HISAT2                   | 2.0.5-intel-2017a                            | Installed on demand.                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| HTSeq                    | 0.7.2-intel-2017a-Python-2.7.13              | Moved into BioTools-Python/2020a.00-intel-2020a-*     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| hwloc                    | 1.11.5-GCC-6.3.0-2.27                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ImageMagick`_           | 7.0.9-7-GCCcore-8.3.0                        | 7.0.10-10-GCCcore-9.3.0                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| intel                    | 2019b                                        | 2020a                                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| inteldevtools            | 2019b                                        | 2020a                                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| IntelPython2             | 2019b                                        | Python 2 support has ended                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| IntelPython3             | 2019b (3.6 equivalent)                       | 2020a (3.7 equivalent)                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `intltool`_              | 0.51.0-intel-2018b-Perl-5.26.1               | 0.51.0-GCCcore-9.3.0-Perl-5.30.2                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `IOzone`_                | 3.489                                        | System maintenance only                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| i-PI                     | /                                            | 2.3.0-intel-2020a-Python-3.8.3                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ITensor`_               | 2.1.1-intel-2018b                            | On demand, not meant for a central install            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `JAGS`_                  | 4.3.0-intel-2019b                            | 4.3.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| JasPer                   | 2.0.14-intel-2018b                           | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Java                     | 11                                           | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Jmol`_                  | 14.30.1-Java-11                              | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Julia`_                 | 0.6.0-intel-2017a-Python-2.7.13              | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `JUnit`_                 | 4.12-Java-8                                  | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Keras`_                 | 2.2.2                                        | Keras is now part of TensorFlow                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| KHRplatform              | 1.0                                          | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Kraken`_                | 1.0-intel-2018b-Perl-5.26.1                  | 1.1.1-intel-2020a-Perl-5.30.2                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Kraken2`_               | /                                            | 2.0.9-beta-intel-2020a-Perl-5.30.2                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `kwant`_                 | 1.2.2-intel-2017a-Python-3.6.1               | Consider kwant-bundle which includes related packages |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| kwant-bundle             | 1.3.2-intel-2018a-Python-3.6.6               | 1.4.2-intel-2020a-Python-3.8.3                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| LAME                     | 3.100-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `LAMMPS`_                | 16Mar2018-intel-2017a                        | 11Aug2017-intel-2020a                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libcerf                  | 1.5-intel-2018b                              | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libffi                   | 3.2.1-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `libgd`_                 | 2.2.5-intel-2019b                            | 2.3.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Libint                   | v2.6.0-intel-2019b-cp2k-lmax-4               | Installed in function of other packages               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libjpeg-turbo            | 1.5.3-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libmatheval              | 1.1.11-intel-2017a                           | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libpng                   | 1.6.34-intel-2018b                           | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libreadline              | 7.0-intel-2018b                              | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| librosa                  | 0.7.2-intel-2019b-Python-3.7.4               | Waiting for compatible version                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libsndfile               | 1.0.28-GCCcore-8.3.0                         | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| LibTIFF                  | 4.0.9-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libtool                  | 2.4.6                                        | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libunistring             | 0.9.8-intel-2018a                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `libvdwxc`_              | 0.4.0-intel-2019b-MPI                        | 0.4.0-intel-2020a-MPI                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `libxc`_                 | 4.3.4-intel-2019b                            | 4.3.4-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libxml2                  | 2.9.8-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libxslt                  | 1.1.32-intel-2018b                           | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `libxsmm`_               | 1.14-intel-2019b                             | 1.15-intel-2020a                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| libyaml                  | 0.2.2-GCCcore-8.3.0                          | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `LittleCMS`_             | 2.9-GCCcore-8.3.0                            | 2.9-GCCcore-9.3.0                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `LLVM`_                  | 3.9.1-intel-2017a                            | In function of other packages                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| LMDB                     | 0.9.22-intel-2018b                           | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Lumen                    | 1.2-intel-2018a                              | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| M4                       | 1.4.18-GCCcore-7.3.0                         | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `MAFFT`_                 | 7.407-intel-2018b-with-extensions            | 7.471-intel-2020a-with-extensions                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `make`_                  | 4.2.1                                        | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Maple`_                 | 2020.0                                       | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Mathematica`_           | 12.0                                         | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `MATLAB`_                | R2020a                                       | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| MCL                      | 14.137-intel-2019b                           | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| mdust                    | 1.0-intel-2017a                              | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| MEGAHIT                  | 1.2.9-intel-2019b                            | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Mesa                     | CentOS7                                      | Dummy module needed for EasyBuild                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| metapub                  | Was Python-bioinformatics                    | 0.5.50intel-2020a-...                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `METIS`_                 | 5.1.0-intel-2019b-i32-fp64                   | 5.1.0-intel-2020a-i32-fp64                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| miniasm                  | /                                            | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| minimap2                 | Not installed but requested                  | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `molmod`_                | 1.1-intel-2017a-Python-2.7.13                | 1.4.7-intel-2020a-...                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| monitor                  | 1.1.2                                        | 1.1.2 (system toolchain)                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Mono                     | 4.8.0.495-intel-2017a                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| MonolixSuite             | 2019R2                                       | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| MPFR                     | 4.0.1-intel-2018b                            | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `MrBayes`_               | 3.2.7-intel-2019b-MPI                        | 3.2.7-intel-2020a-MPI                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `MUMPS`_                 | 5.2.1-intel-2019b-noOpenMP-noMPI             | 5.3.1-intel-2020a-noOpenMP-noMPI                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `MUSCLE`_                | 3.8.31-intel-2019b                           | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `NAMD`_                  | 2.12-verbs, 2.12-verbs-smp                   | 2.14-verbs, 2.14-verbs-smp                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| NASM                     | 2.12.02                                      | Moved to buildtools/2020a                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| ncbi-vdb                 | 2.8.2-intel-2017a                            | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| ncurses                  | 6.1-intel-2018b                              | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `netCDF`_                | 4.7.0-intel-2019b-(no)MPI                    | 4.7.3-intel-2020a-(no)MPI                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| NEST                     | 2.20.1-intel-2019b-Python-3.7.4-\*           | 2.20.1-intel-2020a-Python-3.8.3-\*                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `NetPyNE`_               | 0.9.1.3-intel-2018b-Python-3.7.1             | 0.9.6-intel-2020a-...                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `NEURON`_                | 7.7.2-intel-2019b-Python-3.7.4               | 7.7.2-intel-2020a-Python-3.8.2                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `NGS`_                   | 2.9.6-intel-2019b                            | 2.10.4-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| NSS-NSPR                 | 3.45-4.22-GCCcore-8.3.0                      | 3.51.1-4.25-GCCcore-9.3.0                             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `NTPoly`_                | 2.4-intel-2019b                              | 2.4-intel-2020a                                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| numactl                  | 2.0.11-GCC-6.3.0-2.27                        | Installed with OpenMPI                                |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `numba`_                 | 0.48.0-intel-2019b-Python-3.7.4              | 0.49.1-intel-2020a-Python-3.8.3                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `NWChem`_                | 6.6.r27746-intel-2017a-Python-2.7.13         | 7.0.0-intel-2020a-Python-3.8.3                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `OMNIS-LB`_              | 3.1-2                                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `OpenBLAS`_              | 0.3.5-GCC-7.3.0-2.30                         | Installed with foss                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `OpenCV`_                | 3.4.0-intel-2018a-CPU-noGUI                  | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `OpenFOAM`_              | 6-intel-2019b                                | 6-intel-2020a                                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `OpenMPI`_               | 3.1.1-GCC-7.3.0-2.30                         | Installed with foss                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `OpenMX`_                | 3.8.5-intel-2018b                            | 3.8.5-intel-2020a, 3.9.2-intel-2020a                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| OrthoFinder              | 2.2.6-intel-2018a                            | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| OTF2                     | 2.1.1-intel-2018a                            | Installed when needed                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| p7zip                    | 16.02                                        | SYSTEM toolchain, unmaintained                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Pango`_                 | 1.44.3-GCCcore-8.3.0                         | 1.44.7-GCCcore-9.3.0                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `parallel`_              | 20180422                                     | 20200422                                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ParaView`_              | - 5.4.1-intel-2018a-viz-Python-3.6.4         | Updated on demand, fails to compile so far            |
|                          | - 5.8.1-intel-2018a-viz-Python-3.6.4         |                                                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `ParMETIS`_              | 4.0.3-intel-2019b-i32-fp64                   | 4.0.3-intel-2020a-i32-fp64                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| patchelf                 | 0.9                                          | Moved into buildtools/2020a                           |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| pbs_PRISMS               | 1.0.1-intel-2017a-Python-2.7.13              | Not for SLURM                                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| pbs_python               | 4.6.0-intel-2017a-Python-2.7.13              | Not for SLURM                                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| PCRE                     | 8.42-intel-2018b                             | Moved to baselibs/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Perl`_                  | 5.30.0-GCCcore-8.3.0                         | 5.30.2-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `phonopy`_               | 2.1.2-intel-2018b-Python-3.6.8               | 2.6.1-intel-2020a-...                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Pilon                    | 1.23-Java-11                                 | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| pixman                   | 0.34.0-intel-2018b                           | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| pkg-config               | 0.29.1                                       | Moved into buildtools/2020a                           |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `PLUMED`_                | 2.6.0-intel-2019b                            | 2.6.1-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| PRANK                    | 170427-intel-2018b                           | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `PROJ`_                  | 6.1.1-intel-2019b                            | 7.0.1-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `protobuf`_              | 3.7.1-intel-2018b-Python-3.6.8               | 3.12.3-GCCcore-9.3.0                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Python`_                | 2.7.18, 3.7.4                                | 3.8.2-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Python-bioinformatics    | 2019b.00-\*                                  | / now metapub                                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Python-IDLab-networks    | 2019b.00-\*                                  | Not installed due to problems with gevent             |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Python-IntelMods         | 2019b.00-intel-2019b-Python-3.7.4            | Obsolete, or try IntelPython3                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Qt5`_                   | 5.13.0-GCCcore-8.3.0-noOpenGL                | TODO - unsolved compilation failures                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `QuantumESPRESSO`_       | 6.4.1-intel-2018b-\*                         | 6.4.1-intel-2020a-\*, 6.5-intel-2020a-\*              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| QUIP                     | 180612-intel-2017a                           | Installed on demand due to past comp. problems        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `QuTiP`_                 | 4.3.1-intel-2018b-Python-3.6.8               | QuTiP/4.5.1-intel-2020a-...                           |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `R`_                     | 3.5.1-intel-2018b                            | 4.0.2-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Racon                    | 1.3.3-intel-2018b                            | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| RAxML                    | 8.2.10-intel-2017a-hybrid                    | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `RAxML-NG`_              | 0.9.0-intel-2019b                            | 0.9.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Roary                    | 3.12.0-intel-2018b-Perl-5.26.1               | Incompatible with other software in the toolchain     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Ruby`_                  | 2.4.0                                        | SYSTEM toolchain, updated on demand                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| SAMtools                 | 1.9-intel-2019b                              | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| ScaLAPACK                | 2.0.2-gompi-7.3.0-OpenBLAS-0.2.20            | Installed with foss                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Scalasca`_              | 2.4-intel-2018a                              | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| scikit-umfpack           | 0.3.2-intel-2019b-Python-3.7.4               | Moved to kwant-bundle                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| SCons                    | 3.0.0                                        | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `SCOTCH`_                | 6.0.7-intel-2019b                            | 6.0.7-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| SICER2                   | Installed in user directory                  | Moved into BioTools-Python                            |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Siesta`_                | 4.0-intel-2017a                              | 4.0.2-intel-2020a, 4.1-b4-intel-2020a                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| Simcenter                | 12.02                                        | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| SIONlib                  | 1.7.2-intel-2018a-tools                      | Installed when needed by a package                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `SMALT`_                 | 0.7.6-intel-2019b                            | 0.7.6-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `SPAdes`_                | 3.14.0-intel-2019b-Python-3.7.4              | 3.14.1-intel-2020a-Python-3.8.2                       |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `SQLite`_                | 3.29.0-intel-2019b                           | 3.31.1-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| STAR                     | /                                            | 2.7.6a-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| STAR-CCM+                | 2019.3.1                                     | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Stata`_                 | 15MP                                         | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `SuiteSparse`_           | 5.4.0-intel-2019b-METIS-5.1.0                | 5.7.1-intel-2020a-METIS-5.1.0                         |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `SWIG`_                  | 4.0.0-\*                                     | 4.0.1-\*                                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Szip`_                  | 2.1.1-intel-2018b                            | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Tcl`_                   | 8.6.9-intel-2019b                            | 8.6.10-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `TELEMAC`_               | v8p1r1-intel-2019b                           | v8p1r1-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `TensorFlow`_            | 2.1.0-intel-2019b-*                          | 2.2.0-intel-2020a-*                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `TensorRT`_              | 6.0.1.5-CUDA-10.1.243-cuDNN-7.6.5.32         | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Tk`_                    | 8.6.9-intel-2019b                            | 8.6.10-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| torque-tools             | 1.0.2                                        | Obsolete on SLURM                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Towhee`_                | /                                            | 8.2.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Trimmomatic`_           | 0.39-Java-11                                 | Toolchain-independent                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| UDUNITS                  | 2.2.26-intel-2018b                           | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Unicycler`_             | 0.4.7-intel-2018b-Python-3.7.1               | 0.4.8-intel-2020a-Python-3.8.3                        |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `USPEX`_                 | 10.3-intel-2018a                             | TODO - Needs VASP first                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| util-linux               | 2.32-intel-2018b                             | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `VASP`_                  | 5.4.4-intel-2018b-Wannier90-2.1.0            | - 5.4.4-intel-2020a-Wannier90-2.1.0                   |
|                          |                                              | - 6.1.1-intel-2020a-Wannier90-2.1.0                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| VESTA                    | 3.4.6                                        | Installed on demand                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| VMD                      | 1.9.3-intel-2019b-Python-2.7.16-viz          | 1.9.3-intel-2020a-viz                                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Voro++`_                | 0.4.6-intel-2019b                            | 0.4.6-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| vsc-base                 | 2.5.1                                        | Obsolete                                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| vsc-install              | 0.12.7-intel-2019b-Python-3.7.4              | Obsolete                                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| vsc-mympirun             | 4.1.9-intel-2019b-Python-2.7.16              | 5.0.1 (SYSTEM toolchain)                              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| vsc-tutorial             | 202003-intel-2019b                           | 202003-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| vsc-vnc                  | 0.1                                          | SYSTEM toolchain                                      |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| VSEARCH                  | 2.14.2-intel-2019b                           | Moved into BioTools/2020a.00-intel-2020a              |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Wannier90`_             | 2.1.0-intel-2018b                            | 3.1.0-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `WannierTools`_          | /                                            | 2.5.1-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `worker`_                | 1.6.8-intel-2019b                            | 1.6.12-intel-2020a                                    |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| X11                      | 2019b-GCCcore-8.3.0                          | 2020a-GCCcore-9.3.0                                   |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| x264                     | 20180212-intel-2018b                         | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| x265                     | 2.8-intel-2018b                              | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| XML-LibXML               | 2.0132-intel-2018b-Perl-5.26.1               | Integrated into BioPerl                               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| xprop                    | 1.2.4-GCCcore-8.3.0                          | Integrated in X11/2020a-GCCcore-9.3.0                 |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| XZ                       | 5.2.4-intel-2018b                            | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| `Yambo`_                 | /                                            | 4.4.1-intel-2020a                                     |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| ZDPlasKin                | 2.0a                                         | TODO                                                  |
+--------------------------+----------------------------------------------+-------------------------------------------------------+
| zlib                     | 1.2.11-intel-2018b                           | Moved into baselibs/2020a-GCCcore-9.3.0               |
+--------------------------+----------------------------------------------+-------------------------------------------------------+


Additional information
----------------------

For the modules in alphabetical order:

Python
~~~~~~

We refer to the page :ref:`Python on the UAntwerp clusters <Antwerp Python>` for information
on the differences between various Python modules on our system and on installing additional packages.


R module
~~~~~~~~

The R module in the 2020a toolchain contains roughly 600 R packages from the `CRAN <https://cran.r-project.org/>`_
and `BioConductor <https://www.bioconductor.org/>`_ repositories. The list is based on packages requested by our own
users and by users at some institutions that we collaborate with.

It is possible to install additional packages in your own directory using ``install.packages``.
As for Python, we prefer that Conda is only used as the method-of-last-resort for the same reasons as
given on :ref:`the page "Python on the UAntwerp clusters <Antwerp Python>`.

If you install additional packages yourself and let us know, we will try to add them to the next release of
our R module.