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bedroge merged 1 commit into from
Oct 30, 2026
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update overview of available software #933

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3 changes: 2 additions & 1 deletion docs/available_software/detail/FastQC.md
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Expand Up @@ -50,4 +50,5 @@ pipeline.
|FastQC version|Supported CPU targets|Supported GPU targets|EESSI version|Module|
| --- | --- | --- | --- | --- |
|0.12.1|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`<br/>|*(none)*|<span class="software-eessi-version-202306">2023.06</span>|`FastQC/0.12.1-Java-11`|
|0.12.1|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`, `zen5`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`<br/>|*(none)*|<span class="software-eessi-version-202506">2025.06</span>|`FastQC/0.12.1-Java-11`|
|0.12.1|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`, `zen5`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`<br/>|*(none)*|<span class="software-eessi-version-202506">2025.06</span>|`FastQC/0.12.1-Java-11`|
|0.12.1|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`, `zen5`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`<br/>|*(none)*|<span class="software-eessi-version-202506">2025.06</span>|`FastQC/0.12.1-GCCcore-14.3.0-Java-21`|
1 change: 1 addition & 0 deletions docs/available_software/detail/GATK.md
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Expand Up @@ -47,4 +47,5 @@ The Genome Analysis Toolkit or GATK is a software package developed at the Broad
|GATK version|Supported CPU targets|Supported GPU targets|EESSI version|Module|
| --- | --- | --- | --- | --- |
|4.6.2.0|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`, `aws/graviton4`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`, `zen5`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`, `graniterapids`<br/>|*(none)*|<span class="software-eessi-version-202606">2026.06</span>|`GATK/4.6.2.0-GCCcore-15.2.0-Java-25`|
|4.6.2.0|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`, `zen5`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`<br/>|*(none)*|<span class="software-eessi-version-202506">2025.06</span>|`GATK/4.6.2.0-GCCcore-14.3.0-Java-17`|
|4.5.0.0|`generic`: `aarch64`, `x86_64`<br/><span class="software-cpu-arm">Arm</span>: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`<br/><span class="software-cpu-amd">AMD</span>: `zen2`, `zen3`, `zen4`<br/><span class="software-cpu-intel">Intel</span>: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`<br/>|*(none)*|<span class="software-eessi-version-202306">2023.06</span>|`GATK/4.5.0.0-GCCcore-12.3.0-Java-17`|
33 changes: 17 additions & 16 deletions docs/available_software/detail/R-bundle-CRAN.md
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Expand Up @@ -2479,7 +2479,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`fastGHQuad` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### fastICA

Expand All @@ -2495,7 +2495,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`fastlogranktest` version|R-bundle-CRAN modules that include it|
| --- | --- |
|0.2.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`|
|0.2.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`|

### fastmatch

Expand Down Expand Up @@ -2816,7 +2816,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`frbs` version|R-bundle-CRAN modules that include it|
| --- | --- |
|3.2-0|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|3.2-0|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### fru

Expand Down Expand Up @@ -2992,7 +2992,7 @@ Overview of extensions included in R-bundle-CRAN installations
|`gcmr` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.0.4|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|1.0.3|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.0.3|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### gdalUtils

Expand Down Expand Up @@ -3528,7 +3528,7 @@ Overview of extensions included in R-bundle-CRAN installations
| --- | --- |
|0.5.0|`R-bundle-CRAN/2026.07-foss-2026.1`|
|0.4.0|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|0.3.0|`R-bundle-CRAN/2024.11-foss-2024a`|
|0.3.0|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`|

### gomms

Expand Down Expand Up @@ -3665,6 +3665,7 @@ Overview of extensions included in R-bundle-CRAN installations
|3.9.0|`R-bundle-CRAN/2026.07-foss-2026.1`|
|3.7.0|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|3.6.5|`R-bundle-CRAN/2024.11-foss-2024a`|
|3.6.4|`R-bundle-CRAN/2024.06-foss-2023b`|

### gsl

Expand Down Expand Up @@ -3695,7 +3696,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`gsubfn` version|R-bundle-CRAN modules that include it|
| --- | --- |
|0.7|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|0.7|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### gsw

Expand Down Expand Up @@ -4312,7 +4313,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`kableExtra` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.4.0|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.4.0|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### kde1d

Expand Down Expand Up @@ -5560,7 +5561,7 @@ Overview of extensions included in R-bundle-CRAN installations
| --- | --- |
|1.0.20|`R-bundle-CRAN/2026.07-foss-2026.1`|
|1.0.13|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|1.0.6|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.0.6|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### momentfit

Expand Down Expand Up @@ -5615,7 +5616,7 @@ Overview of extensions included in R-bundle-CRAN installations
| --- | --- |
|1.3|`R-bundle-CRAN/2026.07-foss-2026.1`|
|1.2|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|1.1.1|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.1.1|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### mpoly

Expand Down Expand Up @@ -6189,7 +6190,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`pander` version|R-bundle-CRAN modules that include it|
| --- | --- |
|0.6.6|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|0.6.6|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### paradox

Expand Down Expand Up @@ -6315,7 +6316,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`pbmcapply` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.5.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`|
|1.5.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`|

### PCAmatchR

Expand Down Expand Up @@ -6845,7 +6846,7 @@ Overview of extensions included in R-bundle-CRAN installations

|`PWEALL` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.3.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`|
|1.3.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`|

### qgam

Expand Down Expand Up @@ -7005,7 +7006,7 @@ Overview of extensions included in R-bundle-CRAN installations
| --- | --- |
|1.3.1|`R-bundle-CRAN/2026.07-foss-2026.1`|
|1.2.0|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|1.1.1|`R-bundle-CRAN/2024.11-foss-2024a`|
|1.1.1|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`|

### R2WinBUGS

Expand Down Expand Up @@ -7212,7 +7213,7 @@ Overview of extensions included in R-bundle-CRAN installations
|`RcppNumerical` version|R-bundle-CRAN modules that include it|
| --- | --- |
|0.7-0|`R-bundle-CRAN/2026.07-foss-2026.1`|
|0.6-0|`R-bundle-CRAN/2023.12-foss-2023a`|
|0.6-0|`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### RcppParallel

Expand Down Expand Up @@ -8353,7 +8354,7 @@ Overview of extensions included in R-bundle-CRAN installations
|`sgdGMF` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`<br/>`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`|
|1.0|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.0|`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### shadowtext

Expand Down Expand Up @@ -9263,7 +9264,7 @@ Overview of extensions included in R-bundle-CRAN installations
|`texreg` version|R-bundle-CRAN modules that include it|
| --- | --- |
|1.39.5|`R-bundle-CRAN/2026.07-foss-2026.1`|
|1.39.4|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|
|1.39.4|`R-bundle-CRAN/2025.11-foss-2025b`<br/>`R-bundle-CRAN/2025.10-foss-2025a`<br/>`R-bundle-CRAN/2024.11-foss-2024a`<br/>`R-bundle-CRAN/2024.06-foss-2023b`<br/>`R-bundle-CRAN/2023.12-foss-2023a`|

### textcat

Expand Down
2 changes: 1 addition & 1 deletion mkdocs.yml
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Expand Up @@ -232,7 +232,7 @@ extra:
icon: fontawesome/solid/rss
link: https://eessi.io/docs/feed_json_created.json
# this gets auto-updated via update_generated_time.sh script run in update_available_software.yml action
generated_time: "Thu, 29 Oct 2026 at 17:52:49 UTC"
generated_time: "Fri, 30 Oct 2026 at 17:34:19 UTC"
slack_invite_url: "https://join.slack.com/t/eessi-hpc/shared_invite/zt-2wg10p26d-m_CnRB89xQq3zk9qxf1k3g"
extra_javascript:
# mermaid diagram
Expand Down