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Update available software #597

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Update available software #597

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f90f87e
add code for generating site-packages
Mar 6, 2024
7b418de
remove unecessary print statements
Mar 6, 2024
c7e9f7b
get software paths
Mar 6, 2024
ee2226c
remove hardcoded mapping
Mar 6, 2024
cf643c7
remove hardcoded mapping
Mar 6, 2024
14e182c
resolve CI errors
Mar 6, 2024
6b7a73c
filter packages
Mar 6, 2024
05d3ac4
update tests for updated modules_ugent() funtion
Mar 6, 2024
fcc2613
update tests for updated generate_json_detailed() funtion
Mar 6, 2024
8f349b0
update test for new json_data_detail.json structure
Mar 6, 2024
9ab0084
fix test.sh
Mar 6, 2024
8cccba7
fix test.sh
Mar 6, 2024
3d1feb0
fix trailing whitespace
Mar 6, 2024
8062df3
update available_software to get description, homepage and extensions
Mar 7, 2024
7fa0362
update available_software generated markdown pages
Mar 7, 2024
6683a51
resolve failing CI
Mar 7, 2024
276ca21
add resolve for missing description for some software
Mar 7, 2024
37c275d
resolve failing CI
Mar 7, 2024
e9dc1d4
generate new software pages
Mar 7, 2024
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2 changes: 1 addition & 1 deletion mkdocs/docs/HPC/only/gent/available_software/data/json_data.json
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2 changes: 1 addition & 1 deletion mkdocs/docs/HPC/only/gent/available_software/data/json_data_detail.json
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18 changes: 11 additions & 7 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ABAQUS.md
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ABAQUS
======


Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.

https://www.simulia.com/products/abaqus_fea.html
# Available modules


Expand All @@ -17,11 +21,11 @@ To start using ABAQUS, load one of these modules using a `module load` command l
module load ABAQUS/2023
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABAQUS/2023|x|x|x|x|x|x|x|x|
|ABAQUS/2022-hotfix-2214|-|x|x|-|x|x|x|x|
|ABAQUS/2022|-|x|x|-|x|x|x|x|
|ABAQUS/2021-hotfix-2132|-|x|x|-|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABAQUS/2023|x|x|x|x|x|x|
|ABAQUS/2022-hotfix-2214|-|x|x|-|x|x|
|ABAQUS/2022|-|x|x|-|x|x|
|ABAQUS/2021-hotfix-2132|-|x|x|-|x|x|
16 changes: 10 additions & 6 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ABINIT.md
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ABINIT
======


ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure ofsystems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), usingpseudopotentials and a planewave or wavelet basis.

https://www.abinit.org/
# Available modules


Expand All @@ -17,10 +21,10 @@ To start using ABINIT, load one of these modules using a `module load` command l
module load ABINIT/9.10.3-intel-2022a
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABINIT/9.10.3-intel-2022a|-|-|x|-|x|x|x|x|
|ABINIT/9.4.1-intel-2020b|-|x|x|x|x|x|x|x|
|ABINIT/9.2.1-intel-2020a|-|x|x|-|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABINIT/9.10.3-intel-2022a|-|-|x|-|x|x|
|ABINIT/9.4.1-intel-2020b|-|x|x|x|x|x|
|ABINIT/9.2.1-intel-2020a|-|x|x|-|x|x|
16 changes: 10 additions & 6 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ABRA2.md
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ABRA2
=====


Assembly Based ReAligner

https://github.com/mozack/abra2
# Available modules


Expand All @@ -17,10 +21,10 @@ To start using ABRA2, load one of these modules using a `module load` command li
module load ABRA2/2.23-GCC-10.2.0
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABRA2/2.23-GCC-10.2.0|-|x|x|x|x|x|x|x|
|ABRA2/2.23-GCC-9.3.0|-|x|x|-|x|x|x|x|
|ABRA2/2.22-iccifort-2019.5.281|-|x|-|-|-|-|-|-|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABRA2/2.23-GCC-10.2.0|-|x|x|x|x|x|
|ABRA2/2.23-GCC-9.3.0|-|x|x|-|x|x|
|ABRA2/2.22-iccifort-2019.5.281|-|x|-|-|-|-|
12 changes: 8 additions & 4 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ABRicate.md
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ABRicate
========


Mass screening of contigs for antimicrobial and virulence genes

https://github.com/tseemann/abricate
# Available modules


Expand All @@ -17,8 +21,8 @@ To start using ABRicate, load one of these modules using a `module load` command
module load ABRicate/0.9.9-gompi-2019b
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABRicate/0.9.9-gompi-2019b|-|x|x|-|x|x|-|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABRicate/0.9.9-gompi-2019b|-|x|x|-|x|x|
15 changes: 10 additions & 5 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ABySS.md
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ABySS
=====


Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

https://www.bcgsc.ca/platform/bioinfo/software/abyss
# Available modules


Expand All @@ -14,11 +18,12 @@ The overview below shows which ABySS installations are available per HPC-UGent T
To start using ABySS, load one of these modules using a `module load` command like:

```shell
module load ABySS/2.1.5-foss-2019b
module load ABySS/2.3.7-foss-2023a
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABySS/2.1.5-foss-2019b|-|x|x|-|x|x|-|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ABySS/2.3.7-foss-2023a|x|x|x|x|x|x|
|ABySS/2.1.5-foss-2019b|-|x|x|-|x|x|
12 changes: 8 additions & 4 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ACTC.md
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ACTC
====


ACTC converts independent triangles into triangle strips or fans.

https://sourceforge.net/projects/actc
# Available modules


Expand All @@ -17,8 +21,8 @@ To start using ACTC, load one of these modules using a `module load` command lik
module load ACTC/1.1-GCCcore-10.2.0
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ACTC/1.1-GCCcore-10.2.0|-|x|x|x|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ACTC/1.1-GCCcore-10.2.0|-|x|x|x|x|x|
12 changes: 8 additions & 4 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ADMIXTURE.md
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ADMIXTURE
=========


ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

https://dalexander.github.io/admixture/
# Available modules


Expand All @@ -17,8 +21,8 @@ To start using ADMIXTURE, load one of these modules using a `module load` comman
module load ADMIXTURE/1.3.0
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ADMIXTURE/1.3.0|-|x|x|-|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ADMIXTURE/1.3.0|-|x|x|-|x|x|
35 changes: 35 additions & 0 deletions mkdocs/docs/HPC/only/gent/available_software/detail/AICSImageIO.md
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---
hide:
- toc
---

AICSImageIO
===========


Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python

https://github.com/AllenCellModeling/aicsimageio
# Available modules


The overview below shows which AICSImageIO installations are available per HPC-UGent Tier-2cluster, ordered based on software version (new to old).

To start using AICSImageIO, load one of these modules using a `module load` command like:

```shell
module load AICSImageIO/4.14.0-foss-2022a
```

*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AICSImageIO/4.14.0-foss-2022a|x|x|x|x|x|x|


### AICSImageIO/4.14.0-foss-2022a

This is a list of extensions included in the module:

%(namelower)s-4.14.0, elementpath-4.1.5, fsspec-2023.6.0, ome-zarr-0.8.3, ome_types-0.4.3, pydantic_compat-0.1.2, resource_backed_dask_array-0.1.0, xmlschema-2.5.0, xsdata-23.8
12 changes: 8 additions & 4 deletions mkdocs/docs/HPC/only/gent/available_software/detail/AMAPVox.md
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AMAPVox
=======


LiDAR data voxelisation software

https://amap-dev.cirad.fr/projects/amapvox
# Available modules


Expand All @@ -17,8 +21,8 @@ To start using AMAPVox, load one of these modules using a `module load` command
module load AMAPVox/1.9.4-Java-11
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMAPVox/1.9.4-Java-11|x|x|x|-|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMAPVox/1.9.4-Java-11|x|x|x|-|x|x|
28 changes: 28 additions & 0 deletions mkdocs/docs/HPC/only/gent/available_software/detail/AMICA.md
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---
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- toc
---

AMICA
=====


Code for AMICA: Adaptive Mixture ICA with shared components

https://github.com/sccn/amica
# Available modules


The overview below shows which AMICA installations are available per HPC-UGent Tier-2cluster, ordered based on software version (new to old).

To start using AMICA, load one of these modules using a `module load` command like:

```shell
module load AMICA/2024.1.19-intel-2023a
```

*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMICA/2024.1.19-intel-2023a|x|x|x|x|x|x|
15 changes: 10 additions & 5 deletions mkdocs/docs/HPC/only/gent/available_software/detail/AMOS.md
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AMOS
====


The AMOS consortium is committed to the development of open-source whole genome assembly software

http://amos.sourceforge.net
# Available modules


Expand All @@ -14,11 +18,12 @@ The overview below shows which AMOS installations are available per HPC-UGent Ti
To start using AMOS, load one of these modules using a `module load` command like:

```shell
module load AMOS/3.1.0-foss-2021b
module load AMOS/3.1.0-foss-2023a
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMOS/3.1.0-foss-2021b|x|x|x|-|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMOS/3.1.0-foss-2023a|x|x|x|x|x|x|
|AMOS/3.1.0-foss-2021b|x|x|x|-|x|x|
19 changes: 15 additions & 4 deletions mkdocs/docs/HPC/only/gent/available_software/detail/AMPtk.md
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AMPtk
=====


AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also beused to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial16S, and insect COI amplicons.

https://amptk.readthedocs.io
# Available modules


Expand All @@ -17,8 +21,15 @@ To start using AMPtk, load one of these modules using a `module load` command li
module load AMPtk/1.5.4-foss-2021b
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMPtk/1.5.4-foss-2021b|x|x|x|-|x|x|


### AMPtk/1.5.4-foss-2021b

This is a list of extensions included in the module:

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|AMPtk/1.5.4-foss-2021b|x|x|x|-|x|x|x|x|
amptk-1.5.4, distro-1.7.0, natsort-8.1.0, pyfastx-0.8.4
14 changes: 9 additions & 5 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ANTLR.md
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ANTLR
=====


ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.

https://www.antlr2.org/
# Available modules


Expand All @@ -17,9 +21,9 @@ To start using ANTLR, load one of these modules using a `module load` command li
module load ANTLR/2.7.7-GCCcore-10.3.0-Java-11
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ANTLR/2.7.7-GCCcore-10.3.0-Java-11|-|x|x|-|x|x|x|x|
|ANTLR/2.7.7-GCCcore-8.3.0-Java-11|-|x|x|-|x|x|x|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ANTLR/2.7.7-GCCcore-10.3.0-Java-11|-|x|x|-|x|x|
|ANTLR/2.7.7-GCCcore-8.3.0-Java-11|-|x|x|-|x|x|
12 changes: 8 additions & 4 deletions mkdocs/docs/HPC/only/gent/available_software/detail/ANTs.md
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ANTs
====


ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

https://stnava.github.io/ANTs/
# Available modules


Expand All @@ -17,8 +21,8 @@ To start using ANTs, load one of these modules using a `module load` command lik
module load ANTs/2.3.2-foss-2019b-Python-3.7.4
```

*(This data was automatically generated on Fri, 01 Sep 2023 at 08:52:14 CEST)*
*(This data was automatically generated on Thu, 07 Mar 2024 at 18:35:40 CET)*

| |accelgor|doduo|donphan|gallade|joltik|skitty|swalot|victini|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ANTs/2.3.2-foss-2019b-Python-3.7.4|-|x|x|-|x|x|-|x|
| |accelgor|doduo|donphan|gallade|joltik|skitty|
| :---: | :---: | :---: | :---: | :---: | :---: | :---: |
|ANTs/2.3.2-foss-2019b-Python-3.7.4|-|x|x|-|x|x|
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