Pipeline-Holoruminant-Meta

[boegel]

• link to support ticket: #2025011460002383
• website: https://github.com/fischuu/Pipeline-Holoruminant-Meta
• installation docs: https://github.com/fischuu/Pipeline-Holoruminant-Meta?tab=readme-ov-file#installation
• toolchain: foss/2024a
• easyblock to use: ???
• required dependencies:
  • pandas (SciPy-bundle)
  • snakemake + snakemake-executor-plugin-cluster-generic
• notes:
  • try coming up with instructions on modules to load + commands to run to run this pipeline
    • does it really need a 3TB download?!
  • max effort 2h
• effort: (TBD)
• other install methods
  • conda: no
  • container image: no
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: no

[pavelToman]

I have tried to find all dependencies of Holoruminant-pipeline and it seems it needs this programs/commands:
(!! - not in EB [7x], ** - in EB not for 2023a [11x], OK - should be ready to use)

• R
  rmarkdown - OK
  r-argparse=2.2.2 - OK
  !! r-nonpareil=3.4.0
  r-tidyverse=2.0.0 - OK
  !! r-funr=0.3.2
  r-optparse=1.7.3 - OK

• coreutils=9.3 - maybe no need to have this in deps?

• multiqc=1.18 - OK
  multiqc

• samtools=1.18 - OK
  samtools sort, samtools view, samtools stats, samtools idxstats, samtools collate,
  samtools fast, samtools index, samtools faidx, samtools flagstats

• bowtie2=2.5.1 - OK
  bowtie2-build, bowtie2

• !! coverm=0.6.1
  coverm genome, coverm contig

• ** csvkit=1.3.0
  csvstack, csvformat

• fastp=0.23.4 - OK
  fastp

• fastqc=0.12.1 - OK
  fastqc
  needs Java 11

• gzip=1.10 - OK
  gzip, bgzip, gunzip

• kraken2=2.1.3 - OK
  kraken2

• !! nonpareil=3.4.1
  nonpareil

• pigz=2.8 - OK

• rsync=3.2.7 - OK?

• singlem=0.16.0 - OK
  singlem pipe, singlem condense

• !! dram=1.4.6

• parallel=20230922 - OK? (have 20230722)

• quast=5.2.0 - OK
  quast

• ** vamb==4.1.3
  vamb

• seqtk=1.3 - OK
  seqtk seq

• biopython=1.81 - OK

• ** checkm-genome=1.2.2

• ** drep=3.4.3
  dRep dereplicate

• hmmer=3.3.2 - OK
  hmmsearc

• ** maxbin2=2.2.7

• megahit=1.2.9 - OK
  megahit

• ** metabat2=2.15
  metabat2, jgi_summarize_bam_contig_depths

• pandas=2.1.2 - OK

• prodigal=2.6.3 - OK
  prodigal

• !! rename=1.601
  rename

• ** checkm2=1.0.1
  checkm2 predict

• GTDB-Tk=2.4.0 OK
  classify_wf

• !! Sylph
  sylph profile

• Proteinortho - OK
  proteinortho

• ** PhyloPhlAn
  phylophlan

• ** bakta
  bakta

• Perl - OK
  run_MaxBin.pl, phyloFlash.pl

• Subread - OK
  featureCounts

• ** MetaPhlAn
  metaphlan

• ** HumanN3
  humann

• DIAMOND=2.1.8 - OK
  diamond blastx

[pavelToman]

Time estimation: 23h