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{2023.06}[2023a,2023b] various bioinfo tools #1485

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{2023.06}[2023a,2023b] various bioinfo tools #1485

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{2023.06}[2023a,2023b] various bioinfo tools
jpecar Apr 27, 2026
ed91a6f
{2025.06}[2024a,2025a,2025b,system] various bioinfo tools
jpecar Apr 27, 2026
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7 changes: 7 additions & 0 deletions easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml
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Expand Up @@ -41,3 +41,10 @@ easyconfigs:
include-easyblocks-from-commit: 0f75bae68e0323d7053e0e2dddb03e6422e666e2
# see https://github.com/easybuilders/easybuild-easyconfigs/pull/25220
from-commit: fc6e46c10d6c5d92ea2ab403bfcde364828fa693
- ABySS-2.3.7-foss-2023a.eb
- BUSCO-5.8.2-foss-2023a.eb
- cooltools-0.7.1-foss-2023a.eb
- Trim_Galore-0.6.10-GCCcore-12.3.0.eb
- Kalign-3.4.0-GCCcore-12.3.0.eb
- PyBioLib-1.2.205-GCCcore-12.3.0.eb
- CDBtools-0.99-GCC-12.3.0.eb
8 changes: 7 additions & 1 deletion easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023b.yml
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Expand Up @@ -3,4 +3,10 @@ easyconfigs:
- FEniCS-DOLFINx-Python-0.9.0-foss-2023b.eb:
options:
# see https://github.com/easybuilders/easybuild-easyconfigs/pull/25004
from-commit: 2ef62609e3e40785dfb28bcb91db143cee5924a5
from-commit: 2ef62609e3e40785dfb28bcb91db143cee5924a5
- DIAMOND-2.1.9-GCC-13.2.0.eb
- VSEARCH-2.30.0-GCC-13.2.0.eb
- HH-suite-3.3.0-gompi-2023b.eb
- tabix-0.2.6-GCCcore-13.2.0.eb
- MACS2-2.2.9.1-foss-2023b.eb
- cwltool-3.1.20250110105449-foss-2023b.eb
24 changes: 24 additions & 0 deletions easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.2.0-2024a.yml
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Expand Up @@ -18,3 +18,27 @@ easyconfigs:
# - 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
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@ocaisa ocaisa Apr 27, 2026

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Can you separate out the files targeting 2025.06 into another branch and make a separate PR for those?

- 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
4 changes: 4 additions & 0 deletions easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml
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@@ -1,2 +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
16 changes: 16 additions & 0 deletions easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025a.yml
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Expand Up @@ -2,3 +2,19 @@ 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
20 changes: 20 additions & 0 deletions easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml
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Expand Up @@ -2,3 +2,23 @@ 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
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