{2025.06}[2024a,2025a,2025b,system] various bioinfo tools

Author: jpecar

easystacks/software.eessi.io/eessi-2025.06-eb-5.2.0-2024a.yml

@@ -0,0 +1,44 @@
+easyconfigs:
+  - MLflow-2.22.4-gfbf-2024a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/24951
+        from-commit: 0f50e961c55d6406b0e64eebd59335b32dce0e92
+  - Flux-0.80.0-GCC-13.3.0.eb
+  - WRF-4.6.1-foss-2024a-dmpar.eb
+  - buildenv-default-foss-2024a.eb
+  - GDRCopy-2.4.1-GCCcore-13.3.0.eb
+  - lit-18.1.7-GCCcore-13.3.0.eb
+  - pydot-3.0.3-GCCcore-13.3.0.eb
+  - pyzstd-0.16.2-GCCcore-13.3.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/23923
+        from-commit: 0eef0cf4f6e03172451c41a5af1c0e26b7a777f8
+  - GDB-16.3-GCCcore-13.3.0.eb
+  # Due to a framework problem, these are being built with EB 5.2.0 even when 5.2.1 is available
+  # - framework PR for fix: https://github.com/easybuilders/easybuild-framework/pull/5142
+  # - triggered by https://github.com/easybuilders/easybuild-easyblocks/pull/3993
+  - jupyterlmod-5.2.2-GCCcore-13.3.0.eb
+  - cutadapt-5.1-GCCcore-13.3.0.eb
+  - deepTools-3.5.5-gfbf-2024a.eb
+  - SEPP-4.5.5-foss-2024a.eb
+  - IQ-TREE-3.0.1-gompi-2024a.eb
+  - k8-1.2-GCCcore-13.3.0.eb
+  - HTSeq-2.0.9-foss-2024a.eb
+  - MultiQC-1.28-gfbf-2024a.eb
+  - freebayes-1.3.7-gfbf-2024a-R-4.4.2.eb
+  - SearchGUI-4.3.9-GCCcore-13.3.0-Java-11.eb
+  - StringTie-3.0.0-GCC-13.3.0.eb
+  - Unicycler-0.5.1-gompi-2024a.eb
+  - snpEff-5.4c-GCCcore-13.3.0-Java-21.eb
+  - MUSCLE-5.1.0-GCCcore-13.3.0.eb
+  - GenomeTools-1.6.5-GCC-13.3.0.eb
+  - QUAST-5.3.0-gfbf-2024a.eb
+  - Trinity-2.15.2-foss-2024a-Java-17.eb
+  - PyHMMER-0.12.0-gompi-2024a.eb
+  - vcflib-1.0.9-gfbf-2024a-R-4.4.2.eb
+  - mlst-2.32.2-foss-2024a.eb
+  - GlimmerHMM-3.0.4c-GCC-13.3.0.eb
+  - RGI-6.0.6-gfbf-2024a.eb
+  - MACS3-3.0.3-gfbf-2024a.eb
+  - MetaPhlAn-4.1.1-foss-2024a.eb
+  - Kraken2-2.1.6-gompi-2024a.eb

easystacks/software.eessi.io/eessi-2025.06-eb-5.3.0-001-system.yml

@@ -0,0 +1,6 @@
+easyconfigs:
+  - Julia-1.12.2.eb
+  - picard-3.4.0-Java-21.eb
+  - FastQC-0.12.1-Java-11.eb
+  - Trimmomatic-0.40-Java-17.eb
+  - Nextflow-25.10.2.eb

easystacks/software.eessi.io/eessi-2025.06-eb-5.3.0-2025a.yml

@@ -0,0 +1,20 @@
+easyconfigs:
+  - imageio-2.37.0-gfbf-2025a.eb
+  - scikit-image-0.25.0-foss-2025a.eb
+  - elfutils-0.193-GCCcore-14.2.0.eb
+  - MEME-5.5.9-gompi-2025a.eb
+  - BBMap-39.19-GCC-14.2.0.eb
+  - snakemake-9.14.0-foss-2025a.eb
+  - FastTree-2.2-GCCcore-14.2.0.eb
+  - RAxML-8.2.13-gompi-2025a.eb
+  - pybedtools-0.12.0-foss-2025a.eb
+  - cyvcf2-0.32.1-gfbf-2025a.eb
+  - DendroPy-5.0.8-GCCcore-14.2.0.eb
+  - seqtk-1.5-GCC-14.2.0.eb
+  - VCFtools-0.1.17-GCC-14.2.0.eb
+  - GMAP-GSNAP-2025-07-31-GCC-14.2.0.eb
+  - prodigal-2.6.3-GCCcore-14.2.0.eb
+  - Infernal-1.1.5-gompi-2025a.eb
+  - kallisto-0.51.1-gompi-2025a.eb
+  - prokka-1.15.6-gompi-2025a.eb
+  - snakemake-9.14.0-foss-2025a.eb

easystacks/software.eessi.io/eessi-2025.06-eb-5.3.0-2025b.yml

@@ -0,0 +1,24 @@
+easyconfigs:
+  - Dyninst-13.0.0-GCC-14.3.0.eb
+  - googletest-1.17.0-GCCcore-14.3.0.eb
+  - SciPy-bundle-2025.07-gfbf-2025b.eb
+  - Pysam-0.23.3-GCC-14.3.0.eb
+  - Bowtie2-2.5.4-GCC-14.3.0.eb
+  - HMMER-3.4-gompi-2025b.eb
+  - MAFFT-7.526-GCC-14.3.0-with-extensions.eb
+  - GATK-4.6.2.0-GCCcore-14.3.0-Java-17.eb
+  - ViennaRNA-2.7.2-gfbf-2025b.eb
+  - ncbi-vdb-3.2.1-gompi-2025b.eb
+  - pyfaidx-0.9.0.3-GCCcore-14.3.0.eb
+  - SPAdes-4.2.0-GCC-14.3.0.eb
+  - pyBigWig-0.3.25-gfbf-2025b.eb
+  - fastp-1.1.0-GCC-14.3.0.eb
+  - AUGUSTUS-3.5.0-foss-2025b.eb
+  - SRA-Toolkit-3.2.1-gompi-2025b.eb
+  - BamTools-2.5.3-GCC-14.3.0.eb
+  - MMseqs2-18-8cc5c-gompi-2025b.eb
+  - PyHMMER-0.11.3-gompi-2025b.eb
+  - MEGAHIT-1.2.9-GCCcore-14.3.0.eb
+  - Racon-1.5.0-GCCcore-14.3.0.eb
+  - CD-HIT-4.8.1-GCC-14.3.0.eb
+  - Alfred-0.5.3-GCC-14.3.0.eb