From 2c87ccdcc49c917b2b9785290395d43831c0f21d Mon Sep 17 00:00:00 2001 From: Coldfront Date: Fri, 26 Aug 2022 09:00:22 +0000 Subject: [PATCH] Software table update --- docs/software/01table.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/docs/software/01table.md b/docs/software/01table.md index 50a4666..8174235 100644 --- a/docs/software/01table.md +++ b/docs/software/01table.md @@ -50,7 +50,7 @@ | libtirpc | Libtirpc is a port of Suns Transport-Independent RPC library to Linux. |
TINKERCLIFFS
1.3.2-GCCcore-10.3.0
| TopHat | TopHat is a fast splice junction mapper for RNA-Seq reads. |
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2.1.2-iimpi-2019b
| cytosim | Cytosim is a cytoskeleton simulation engine written in
C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). |
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20190117-gomkl-2019a-mkl
-| networkx | NetworkX is a Python package for the creation, manipulation,
and study of the structure, dynamics, and functions of complex networks. |
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2.4-foss-2020a-Python-3.8.2
+| beagle-lib | BEAGLE-lib |
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3.1.2-GCC-10.2.0
CASCADES
2.1.2
DRAGONSTOOTH
2.1.2
| double-conversion | Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. |
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3.1.5-GCCcore-10.2.0
3.1.4-GCCcore-8.3.0
3.1.5-GCCcore-10.3.0
3.1.5-GCCcore-9.3.0
| x264 | x264 |
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20191217-GCCcore-9.3.0
20190925-GCCcore-8.3.0
20210414-GCCcore-10.3.0
20201026-GCCcore-10.2.0
CASCADES
7.5.2020
1.0
DRAGONSTOOTH
7.5.2020
1.0
| x265 |
x265 is a free software library and application for encoding video streams
into the H.265 AVC compression format, and is released under the terms of
the GNU GPL.
|
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3.2-GCCcore-8.3.0
3.5-GCCcore-10.3.0
3.3-GCCcore-9.3.0
3.3-GCCcore-10.2.0
@@ -82,6 +82,7 @@ | Hypre | Hypre is a library for solving large, sparse linear systems of equations on massively
parallel computers. The problems of interest arise in the simulation codes being developed at LLNL
and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. |
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2.18.2-intel-2019b
| freetype |
FreeType 2 is a software font engine that is designed to be small, efficient,
highly customizable, and portable while capable of producing high-quality
output (glyph images). It can be used in graphics libraries, display servers,
font conversion tools, text image generation tools, and many other products
as well.
|
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2.10.1-GCCcore-9.3.0
2.10.1-GCCcore-8.3.0
2.9.1-GCCcore-8.2.0
2.10.4-GCCcore-10.3.0
2.10.3-GCCcore-10.2.0
| Ghostscript | Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to
different targets. It used to be part of the cups printing stack, but is no longer used for that. |
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9.53.3-GCCcore-10.2.0
9.52-intel-2019b
9.52-GCCcore-9.3.0
9.54.0-GCCcore-10.3.0
+| utf8proc | utf8proc is a small, clean C library that provides Unicode normalization, case-folding,
and other operations for data in the UTF-8 encoding. |
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2.5.0-GCCcore-10.2.0
| nettle | Nettle is a cryptographic library that is designed to fit easily
in more or less any context: In crypto toolkits for object-oriented
languages (C++, Python, Pike, ...), in applications like LSH or GNUPG,
or even in kernel space. |
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3.4.1-GCCcore-8.2.0
3.7.2-GCCcore-10.3.0
3.6-GCCcore-10.2.0
3.5.1-GCCcore-8.3.0
| VirtualGL | VirtualGL is an open source toolkit that gives any Linux or
Unix remote display software the ability to run OpenGL applications with full
hardware acceleration. |
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2.6.2-GCCcore-9.3.0
| aspect-2.2.0 | AspectDESCRIPTION |
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intel-2019b
@@ -148,6 +149,7 @@ | LibTIFF | tiff: Library and tools for reading and writing TIFF data files |
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4.1.0-GCCcore-9.3.0
4.2.0-GCCcore-10.3.0
4.0.10-GCCcore-8.3.0
4.1.0-GCCcore-8.3.0
4.1.0-GCCcore-10.2.0
| gomkl | GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL |
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2020a
2021a
2019a
2020b
| APR-util | Apache Portable Runtime (APR) util libraries. |
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1.6.1-GCCcore-10.2.0
+| pocl | Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard |
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1.6-GCC-10.2.0
| OpenBLAS | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
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0.3.9-GCC-9.3.0
0.3.12-GCC-10.2.0
0.3.15-GCC-10.3.0
| molmod | MolMod is a Python library with many compoments that are useful to write molecular modeling programs. |
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1.4.5-foss-2020a-Python-3.8.2
| libpng | libpng is the official PNG reference library |
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1.6.36-GCCcore-8.2.0
1.6.37-GCCcore-10.2.0
1.6.37-GCCcore-8.3.0
1.6.37-GCCcore-10.3.0
1.6.37-GCCcore-9.3.0
@@ -188,6 +190,7 @@ | prodigal | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm |
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2.6.3-GCCcore-10.2.0
| PROJ | Program proj is a standard Unix filter function which converts
geographic longitude and latitude coordinates into cartesian coordinates |
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7.0.0-GCCcore-9.3.0
8.0.1-GCCcore-10.3.0
| picard | Picard: A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats |
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2.21.6-Java-11
DRAGONSTOOTH
1.138
+| networkx | NetworkX is a Python package for the creation, manipulation,
and study of the structure, dynamics, and functions of complex networks. |
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2.4-foss-2020a-Python-3.8.2
| dealii-9.2.0 | SOFTWAREDESCRIPTION |
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intel-2019b
| pkg-config |
pkg-config is a helper tool used when compiling applications and libraries.
It helps you insert the correct compiler options on the command line so an
application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0`
for instance, rather than hard-coding values on where to find glib (or other
libraries).
|
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0.29.2-GCCcore-8.3.0
0.29.2-GCCcore-10.2.0
0.29.2-GCCcore-8.2.0
0.29.2-GCCcore-10.3.0
0.29.2-GCCcore-9.3.0
| SLEPc | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution
of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for
either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a
partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. |
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3.12.2-intel-2019b
@@ -197,6 +200,7 @@ | libglvnd | libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. |
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1.3.3-GCCcore-10.3.0
1.3.2-GCCcore-10.2.0
1.2.0-GCCcore-9.3.0
1.2.0-GCCcore-8.3.0
| ImageMagick | ImageMagick |
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7.0.10-35-GCCcore-10.2.0
7.0.10-1-intel-2019b
7.0.10-1-GCCcore-9.3.0
7.0.11-14-GCCcore-10.3.0
CASCADES
6.8.9
7.0.10
DRAGONSTOOTH
7.1.0
| PyCharm | PyCharm Community Edition: Python IDE for Professional Developers |
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2021.1.1
2019.3.1
+| MrBayes | MrBayes is a program for Bayesian inference and model choice across
a wide range of phylogenetic and evolutionary models. |
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3.2.7-gompi-2020b
| SWIG | SWIG is a software development tool that connects programs written in C and C++ with
a variety of high-level programming languages. |
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4.0.1-GCCcore-9.3.0
4.0.1-GCCcore-8.3.0
| ATK |
ATK provides the set of accessibility interfaces that are implemented by other
toolkits and applications. Using the ATK interfaces, accessibility tools have
full access to view and control running applications.
|
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2.36.0-GCCcore-9.3.0
2.36.0-GCCcore-10.2.0
| libGLU | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
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9.0.0-GCCcore-8.2.0
9.0.1-GCCcore-10.2.0
9.0.1-GCCcore-8.3.0
9.0.1-GCCcore-10.3.0
9.0.1-GCCcore-9.3.0
@@ -216,6 +220,7 @@ | typing-extensions | Typing Extensions – Backported and Experimental Type Hints for Python |
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3.7.4.3-GCCcore-10.2.0
| impi | Intel MPI Library, compatible with MPICH ABI |
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2021.2.0-intel-compilers-2021.2.0
2019.9.304-iccifort-2020.4.304
2018.5.288-iccifort-2019.5.281
| bokeh | Statistical and novel interactive HTML plots for Python |
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2.0.2-foss-2020a-Python-3.8.2
2.2.3-foss-2020b-Python-3.8.6
+| Clang | C, C++, Objective-C compiler, based on LLVM. Does not
include C++ standard library -- use libstdc++ from GCC. |
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11.0.1-GCCcore-10.2.0
| WPS | WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is
a next-generation mesoscale numerical weather prediction system designed to serve both operational
forecasting and atmospheric research needs. |
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4.2-foss-2020b-dmpar
| kim-api | Open Knowledgebase of Interatomic Models.

KIM is an API and OpenKIM is a collection of interatomic models (potentials) for
atomistic simulations. This is a library that can be used by simulation programs
to get access to the models in the OpenKIM database.

This EasyBuild only installs the API, the models can be installed with the
package openkim-models, or the user can install them manually by running
kim-api-collections-management install user MODELNAME
or
kim-api-collections-management install user OpenKIM
to install them all.
|
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2.1.3-foss-2020a
| HTSlib | A C library for reading/writing high-throughput sequencing data.
This package includes the utilities bgzip and tabix |
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1.11-GCC-10.2.0
1.10.2-GCC-9.3.0
@@ -311,7 +316,7 @@ | pixman |
Pixman is a low-level software library for pixel manipulation, providing
features such as image compositing and trapezoid rasterization. Important
users of pixman are the cairo graphics library and the X server.
|
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0.40.0-GCCcore-10.2.0
0.38.4-GCCcore-8.3.0
0.38.4-GCCcore-9.3.0
0.40.0-GCCcore-10.3.0
| NSS | Network Security Services (NSS) is a set of libraries designed to support cross-platform development
of security-enabled client and server applications. |
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3.65-GCCcore-10.3.0
3.51-GCCcore-9.3.0
3.45-GCCcore-8.3.0
| BUSCO | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs |
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5.0.0-foss-2020b
-| utf8proc | utf8proc is a small, clean C library that provides Unicode normalization, case-folding,
and other operations for data in the UTF-8 encoding. |
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2.5.0-GCCcore-10.2.0
+| Z3 |
Z3 is a theorem prover from Microsoft Research.
|
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4.8.10-GCCcore-10.2.0
| ncdf4 | ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files |
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1.17-foss-2020b-R-4.0.3
| GObject-Introspection | GObject introspection is a middleware layer between C libraries
(using GObject) and language bindings. The C library can be scanned at
compile time and generate a metadata file, in addition to the actual
native C library. Then at runtime, language bindings can read this
metadata and automatically provide bindings to call into the C library. |
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1.66.1-GCCcore-10.2.0
1.63.1-GCCcore-8.3.0-Python-3.7.4
1.68.0-GCCcore-10.3.0
1.64.0-GCCcore-9.3.0-Python-3.8.2
| PyYAML | PyYAML is a YAML parser and emitter for the Python programming language. |
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5.3.1-GCCcore-10.2.0
5.1.2-GCCcore-8.3.0
5.3-GCCcore-9.3.0
@@ -367,7 +372,6 @@ | cudnn | cuDNN | GPU-accelerated library for deep neural networks |
CASCADES
7.0
7.1
HUCKLEBERRY
7.6.5
| tcl | Tool command language |
CASCADES
8.6.9
| netcdf | Network Common Data Form |
CASCADES
4.3.3.1
4.1.3
DRAGONSTOOTH
4.3.3.1
HUCKLEBERRY
4.3.3.1
-| beagle-lib | BEAGLE-lib |
CASCADES
2.1.2
DRAGONSTOOTH
2.1.2
| mysql | MySQL: a very fast and reliable SQL database server |
CASCADES
5.6.14
DRAGONSTOOTH
5.6.14
5.5.37
| LBPM | Lattice Boltzmann simulator |
CASCADES
4.9.2018
| singularity | Singularity is an open source container platform designed to be simple, fast, and secure. |
CASCADES
3.3.0
3.7.3
3.5.1
DRAGONSTOOTH
3.3.0
3.5.1
HUCKLEBERRY
3.3.0
3.5.1