From 43cdb6f7539e4fb763b3d1d2d6cb04dbfd9f64c5 Mon Sep 17 00:00:00 2001
From: EESSIbot <90030231+EESSIbot@users.noreply.github.com>
Date: Fri, 30 Oct 2026 17:34:20 +0000
Subject: [PATCH] update overview of available software
---
docs/available_software/detail/FastQC.md | 3 +-
docs/available_software/detail/GATK.md | 1 +
.../detail/R-bundle-CRAN.md | 33 ++++++++++---------
mkdocs.yml | 2 +-
4 files changed, 21 insertions(+), 18 deletions(-)
diff --git a/docs/available_software/detail/FastQC.md b/docs/available_software/detail/FastQC.md
index 6b9ad5ec3e..4353d4809d 100644
--- a/docs/available_software/detail/FastQC.md
+++ b/docs/available_software/detail/FastQC.md
@@ -50,4 +50,5 @@ pipeline.
|FastQC version|Supported CPU targets|Supported GPU targets|EESSI version|Module|
| --- | --- | --- | --- | --- |
|0.12.1|`generic`: `aarch64`, `x86_64`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`
AMD: `zen2`, `zen3`, `zen4`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`
|*(none)*|2023.06|`FastQC/0.12.1-Java-11`|
-|0.12.1|`generic`: `aarch64`, `x86_64`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`
AMD: `zen2`, `zen3`, `zen4`, `zen5`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`
|*(none)*|2025.06|`FastQC/0.12.1-Java-11`|
\ No newline at end of file
+|0.12.1|`generic`: `aarch64`, `x86_64`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`
AMD: `zen2`, `zen3`, `zen4`, `zen5`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`
|*(none)*|2025.06|`FastQC/0.12.1-Java-11`|
+|0.12.1|`generic`: `aarch64`, `x86_64`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`
AMD: `zen2`, `zen3`, `zen4`, `zen5`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`
|*(none)*|2025.06|`FastQC/0.12.1-GCCcore-14.3.0-Java-21`|
\ No newline at end of file
diff --git a/docs/available_software/detail/GATK.md b/docs/available_software/detail/GATK.md
index 277b9eb6a7..af374db702 100644
--- a/docs/available_software/detail/GATK.md
+++ b/docs/available_software/detail/GATK.md
@@ -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`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`, `aws/graviton4`
AMD: `zen2`, `zen3`, `zen4`, `zen5`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`, `graniterapids`
|*(none)*|2026.06|`GATK/4.6.2.0-GCCcore-15.2.0-Java-25`|
+|4.6.2.0|`generic`: `aarch64`, `x86_64`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`
AMD: `zen2`, `zen3`, `zen4`, `zen5`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`
|*(none)*|2025.06|`GATK/4.6.2.0-GCCcore-14.3.0-Java-17`|
|4.5.0.0|`generic`: `aarch64`, `x86_64`
Arm: `a64fx`, `neoverse_n1`, `neoverse_v1`, `nvidia/grace`
AMD: `zen2`, `zen3`, `zen4`
Intel: `haswell`, `skylake_avx512`, `sapphirerapids`, `icelake`, `cascadelake`
|*(none)*|2023.06|`GATK/4.5.0.0-GCCcore-12.3.0-Java-17`|
\ No newline at end of file
diff --git a/docs/available_software/detail/R-bundle-CRAN.md b/docs/available_software/detail/R-bundle-CRAN.md
index b9c488a49f..e7d272d9c3 100644
--- a/docs/available_software/detail/R-bundle-CRAN.md
+++ b/docs/available_software/detail/R-bundle-CRAN.md
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### fastICA
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`|
+|0.2.1|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`|
### fastmatch
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|3.2-0|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### fru
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`|
-|1.0.3|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.0.3|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### gdalUtils
@@ -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`
`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`
`R-bundle-CRAN/2024.06-foss-2023b`|
### gomms
@@ -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`
`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
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|0.7|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### gsw
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.4.0|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### kde1d
@@ -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`
`R-bundle-CRAN/2025.10-foss-2025a`|
-|1.0.6|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.0.6|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### momentfit
@@ -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`
`R-bundle-CRAN/2025.10-foss-2025a`|
-|1.1.1|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.1.1|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### mpoly
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|0.6.6|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### paradox
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`|
+|1.5.1|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`|
### PCAmatchR
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`|
+|1.3.0.1|`R-bundle-CRAN/2026.07-foss-2026.1`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`|
### qgam
@@ -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`
`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`
`R-bundle-CRAN/2024.06-foss-2023b`|
### R2WinBUGS
@@ -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`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### RcppParallel
@@ -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`
`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`|
-|1.0|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.0|`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### shadowtext
@@ -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`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2023.12-foss-2023a`|
+|1.39.4|`R-bundle-CRAN/2025.11-foss-2025b`
`R-bundle-CRAN/2025.10-foss-2025a`
`R-bundle-CRAN/2024.11-foss-2024a`
`R-bundle-CRAN/2024.06-foss-2023b`
`R-bundle-CRAN/2023.12-foss-2023a`|
### textcat
diff --git a/mkdocs.yml b/mkdocs.yml
index b1b0cf18cc..c3dc362c73 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -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