update Noble Module list

FredHutch · Oct 9, 2024 · 6da832b · 6da832b
1 parent 4f41dce
commit 6da832b
Show file tree

Hide file tree

Showing 6 changed files with 542 additions and 117 deletions.
diff --git a/docs/all-modules-24.04.md b/docs/all-modules-24.04.md
diff --git a/docs/bio-modules-24.04.md b/docs/bio-modules-24.04.md
@@ -2,7 +2,7 @@
 title: Bio Modules 24.04
 layout: single
 permalink: /bio-modules-24.04/
-created: 2024-10-07
+created: 2024-10-08
 toc: true
 toc_label: "On This Page"
 sidebar:
@@ -60,7 +60,7 @@ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
  - [Bio-DB-HTS/3.01-GCC-12.2.0](https://metacpan.org/release/Bio-DB-HTS)
 [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb)
 Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
- - [BioPerl/1.7.8-GCCcore-12.3.0](https://bioperl.org/)
+ - [BioPerl/1.7.8-GCCcore-12.2.0](http://www.bioperl.org/)
 Bioperl is the product of a community effort to produce Perl code which is useful in biology.
  Examples include Sequence objects, Alignment objects and database searching objects.
  - [Biopython/1.84-foss-2023b](https://www.biopython.org)
@@ -108,7 +108,7 @@ stand-alone executable version is also available.
 [easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-13.2.0.eb)
 CoinUtils (Coin-OR Utilities) is an open-source collection of classes and
 functions that are generally useful to more than one COIN-OR project.
- - [Eigen/3.4.0-GCCcore-12.3.0](https://eigen.tuxfamily.org)
+ - [Eigen/3.4.0-GCCcore-13.2.0](https://eigen.tuxfamily.org)
 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers,
  and related algorithms.
  - [FASTA/36.3.8i-GCC-12.2.0](https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml)
@@ -239,7 +239,7 @@ PyTorch with compatible versions of official Torch extensions.
  - [Pysam/0.22.0-GCC-12.3.0](https://github.com/pysam-developers/pysam)
 Pysam is a python module for reading and manipulating Samfiles.
  It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
- - [Qhull/2020.2-GCCcore-12.2.0](http://www.qhull.org)
+ - [Qhull/2020.2-GCCcore-13.2.0](http://www.qhull.org)
 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram,
  halfspace intersection about a point, furthest-site Delaunay triangulation,
  and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and
@@ -281,7 +281,8 @@ Sambamba is a high performance modern robust and fast tool
  (and library), written in the D programming language, for working with SAM
  and BAM files. Current functionality is an important subset of samtools
  functionality, including view, index, sort, markdup, and depth.
- - [Seaborn/0.13.2-gfbf-2023a](https://seaborn.pydata.org/)
+ - [Seaborn/0.13.2-gfbf-2023b](https://seaborn.pydata.org/)
+[easyconfig](https://github.com/FredHutch/easybuild-life-sciences/blob/master/fh_easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023b.eb)
 Seaborn is a Python visualization library based on matplotlib.
  It provides a high-level interface for drawing attractive statistical graphics. 
  - [Shapely/2.0.1-gfbf-2023a](https://github.com/Toblerity/Shapely)

diff --git a/fh_easyconfigs/g/Graphviz/Graphviz-10.0.1-GCCcore-13.2.0.eb b/fh_easyconfigs/g/Graphviz/Graphviz-10.0.1-GCCcore-13.2.0.eb
@@ -17,7 +17,8 @@ source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['%(name)s-8.1.0_skip-install-data-hook.patch']
 checksums = [
-    # {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'},
+    {'graphviz-10.0.1.tar.gz': '28f452ef1cb12288c8758a62f8c3fcfefdb91b251f7aae61d0d703f851bde931'},
+    {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'},
 ]
 
 builddependencies = [

diff --git a/fh_easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb b/fh_easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb
diff --git a/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb b/fh_easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023b.eb
@@ -21,7 +21,7 @@ builddependencies = [
 
 dependencies = [
     ('Python', '3.11.5'),
-    ('igraph', '0.10.10'),
+    ('igraph', '0.10.12'),
     ('python-igraph', '0.11.4'),
     ('libleidenalg', '0.11.1'),
 ]

diff --git a/fh_easyconfigs/r/RStudio-Server/RStudio-Server-2024.04.1+748-foss-2023b-Java-11-R-4.4.0.eb b/fh_easyconfigs/r/RStudio-Server/RStudio-Server-2024.04.1+748-foss-2023b-Java-11-R-4.4.0.eb
@@ -34,7 +34,7 @@ builddependencies = [
 
 dependencies = [
     ('Boost', '1.83.0'),
-    ('GDAL', '3.8.4'),
+    ('GDAL', '3.9.0'),
     ('Java', '11', '', SYSTEM),
     ('R', '4.4.0'),
     ('SOCI', '4.0.3', '-Boost-1.83.0'),